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Crystal structure of Arabidopsis thaliana HPPK/DHPS,a bifunctional enzyme and target of the herbicide asulam

Plant Communications 2022年第4期3卷 137-149页

作者： Grishma vadlamani kirill v.sukhoverkov Joel Haywood Karen J.Breese Mark F.Fisher Keith A.Stubbs Charles S.Bond Joshua S.Mylne School of Molecular Sciences The University of Western Australia35 Stirling HighwayCrawleyWA 6009Australia The ARC Centre of Excellence in Plant Energy Biology The University of Western Australia35 Stirling HighwayCrawleyWA 6009Australia Centre for Crop and Disease Management School of Molecular and Life SciencesCurtin UniversityBentleyWA 6102Australia

Herbicides are vital formodern agriculture,but their utility is threatened by genetic or metabolic resistance in weeds,as well as regulatory *** the known herbicide modes of action,7,8-dihydropterin synthase(DHPS),which is involved in folate biosynthesis,is targeted by just one commercial herbicide,asulam.A mimic of the substrate para-aminobenzoic acid,asulam is chemically similar to sulfonamide antibiotics,and although it is still in widespread use,asulam has faced regulatory *** an entire mode of action represented by just one commercial agrochemical,we sought to improve the understanding of its plant *** we solve a 2.3A°resolution crystal structure for Arabidopsis thaliana DHPS that is conjoined to 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase(HPPK),and we reveal a strong structural conservation with bacterial counterparts at the sulfonamide-bindingpocket of *** demonstrate that asulamand the antibiotic sulfamethoxazole have herbicidal as well as antibacterial activity,andwe explore the structural basis of their potency by modeling these compounds in mitochondrial HPPK/*** findings suggest limited opportunity for the rational design of plant selectivity fromasulamand indicate that pharmacokinetic or delivery differences between plants andmicrobesmight be the bestways to safeguard thismode of action.

关键词： structural biology folate metabolism mode of action

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Anomalies in the short-range local environment and atomic diffusion in single crystalline equiatomic CrMnFeCoNi highentropy alloy

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Nano Research 2024年第6期17卷 5336-5348页

作者： Alevtina Smekhova Daniel Gaertner Alexei Kuzmin Ana Guilherme Buzanich Goetz Schuck Ivo Zizak Gerhard Wilde kirill v.Yusenko Sergiy Divinski Helmholtz-Zentrum Berlin für Materialien und Energie(HZB) D-12489 BerlinGermany Institute of Materials Physics University of MünsterD-48149 MünsterGermany Institute of Solid State Physics University of LatviaLV-1063 RigaLatvia Bundesanstalt für Materialforschung und–prüfung(BAM) D-12489 BerlinGermany

Multi-edge extended X-ray absorption fine structure(EXAFS)spectroscopy combined with reverse Monte Carlo(RMC)simulations was used to probe the details of element-specific local coordinations and component-dependent structure relaxations in single crystalline equiatomic CrMnFeCoNi high-entropy alloy as a function of the annealing *** representative states,namely a high-temperature state,created by annealing at 1373 K,and a low-temperature state,produced by long-term annealing at 993 K,were compared in *** features identified in atomic configurations of particular principal components indicate variations in the local environment distortions connected to different degrees of compositional disorder at the chosen representative *** detected changes provide new atomistic insights and correlate with the existence of kinks previously observed in the Arrhenius dependencies of component diffusion rates in the CrMnFeCoNi high-entropy alloy.

关键词： high-entropy alloys diffusion short-range order extended X-ray absorption fine structure(EXAFS) reverse Monte Carlo

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Exploring van der Waals materials with high anisotropy:geometrical and optical approaches

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Light(Science & Applications) 2024年第4期13卷 645-653页

作者： Aleksandr S.Slavich Georgy A.Ermolaev Mikhail K.Tatmyshevskiy Adilet N.Toksumakov Olga G.Matveeva Dmitriy v.Grudinin kirill v.voronin Arslan Mazitov Konstantin v.Kravtsov Alexander v.Syuy Dmitry M.Tsymbarenko Mikhail S.Mironov Sergey M.Novikov Ivan Kruglov Davit A.Ghazaryan Andrey A.vyshnevyy Aleksey v.Arsenin valentyn S.volkov Kostya S.Novoselov Moscow Center for Advanced Studies Kulakova str.20Moscow 123592Russia. Emerging Technologies Research Center XPANCEOInternet CityEmmay TowerDubaiUnited Arab Emirates. Donostia International Physics Center(DIPC) Donostia/San-Sebastián 20018Spain. Institute of Materials Ecole Polytechnique Federale de Lausanne1015 LausanneSwitzerland. Department of Chemistry Lomonosov Moscow State UniversityMoscow 119991Russia. Laboratory of Advanced Functional Materials Yerevan State UniversityYerevan 0025Armenia. National Graphene Institute(NGI) University of ManchesterManchester M139PLUK. Department of Materials Science and Engineering National University of SingaporeSingapore 03-09 EASingapore. Institute for Functional Intelligent Materials National University of Singapore117544 SingaporeSingapore

The emergence of van der Waals(vdW)materials resulted in the discovery of their high optical,mechanical,and electronic anisotropic properties,immediately enabling countless novel phenomena and *** success inspired an intensive search for the highest possible anisotropic properties among vdW ***,the identification of the most promising among the huge family of vdW materials is a challenging quest requiring innovative ***,we suggest an easy-to-use method for such a survey based on the crystallographic geometrical perspective of vdW materials followed by their optical *** our approach,we found As2S3 as a highly anisotropic vdW *** demonstrates high in-plane optical anisotropy that is~20%larger than for rutile and over two times as large as calcite,high refractive index,and transparency in the visible range,overcoming the century-long record set by *** these benefits,As2S3 opens a pathway towards nextgeneration nanophotonics as demonstrated by an ultrathin true zero-order quarter-wave plate that combines classical and the Fabry–Pérot optical phase ***,our approach provides an effective and easy-to-use method to find vdW materials with the utmost anisotropic properties.

关键词： anisotropy anisotropic high

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A NUMERICAL METHOD FOR THE SIMULATION OF FREE SURFACE FLOWS OF vISCOPLASTIC FLUID IN 3D

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Journal of Computational Mathematics 2011年第6期29卷 605-622页

作者： kirill D. Nikitin Maxim A. Olshanskii kirill M. Terekhov Yuri v. vassilevski Institute of Numerical Mathematics Russian Academy of Sciences Moscow Russia Department of Mechanics and Mathematics Moscow State University Moscow Russia

In this paper we study a numerical method for the simulation of free surface flows of viscoplastic （Herschel-Bulkley） fluids. The approach is based on the level set method for capturing the free surface evolution and on locally refined and dynamically adapted octree cartesian staggered grids for the discretization of fluid and level set equations. A regu- larized model is applied to handle the non-differentiability of the constitutive relations. We consider an extension of the stable approximation of the Newtonian flow equations on staggered grid to approximate the viscoplastic model and level-set equations if the free boundary evolves and the mesh is dynamically refined or coarsened. The numerical method is first validated for a Newtonian case. In this case, the convergence of numerical solutions is observed towards experimental data when the mesh is refined. Further we compute several 3D viscoplastic Herschel-Bulkley fluid flows over incline planes for the dam-break problem. The qualitative comparison of numerical solutions is done versus experimental investigations. Another numerical example is given by computing the freely oscillating viscoplastic droplet, where the motion of fluid is driven by the surface tension forces. Altogether the considered techniques and algorithms （the level-set method, compact discretizations on dynamically adapted octree cartesian grids, regularization, and the surface tension forces approximation） result in efficient approach to modeling viscoplastic free-surface flows in possibly complex 3D geometries.

关键词： Free surface flows viscoplastic fluid Adaptive mesh refinement Oetree meshes.

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LIvE IMAGING OF EARLY DEvELOPMENTAL PROCESSES IN MAMMALIAN EMBRYOS WITH OPTICAL COHERENCE TOMOGRAPHY

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Journal of Innovative Optical Health Sciences 2009年第3期2卷 253-259页

作者： kirill v.LARIN IRINA v.LARINA MICHAEL LIEBLING MARY E.DICKINSON Department of Biomedical Engineering University of Houston HoustonTXUSA Department of Molecular Physiology and Biophysics Baylor College of Medicine HoustonTXUSA Department of Electrical and Computer Engineering University of California Santa BarbaraCAUSA

Early embryonic imaging of cardiovascular development in mammalian models requires a methodthat can penetrate through and distinguish the many tissue layers with high spatial and temporalresolution. In this paper we evaluate the capability of Optical Coherence Tomography (OCT)technique for structural 3D embryonic imaging in mouse embryos at different stages of thedevelopmental process ranging from 7.5 dpc up to 10.5 dpc. Obtained results suggest that thecollected data is suitable for quantitative and qualitative measurements to assess cardiovascularfunction in mouse models, which is likely to expand our knowledge of the complexity of theembryonic heart, and its development into an adult heart.

关键词： Optical Coherence Tomography non-invasive mouse embryos cardiovascular function.

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FOREWORD

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Journal of Innovative Optical Health Sciences 2009年第1期2卷 I0001-I0002页

作者： Elina A.Genina kirill v.Larin valery v.Tuchin Research-Educational Institute of Optics and Biophotonics Saratov State University Saratov Russia Department of Biomedical Engineering University of Houston Houston USA Research-Educational Institute of Optics and Biophotonics Saratov State University Institute of Precise Mechanics and Control RAS Saratov Russia

Special Issue Optical Technologies in the Study of Tissues and Biological Fluids We are pleased to present this special issue of JIOHS,which focuses on optical technologies in the study of tissues and biological *** selected papers were presented during Saratov Fall Meeting—XII International School for Junior Scientists and Students on Optics,Laser Physics and Biophotonics(September 23–26,2008,Saratov,Russia)in the framework of the following workshops:“Optical Technologies in Biophysics and Medicine,”“Nanostructures and Nanoparticles,”“Microscopic and Low-Coherence Methods in Biomedical Applications,”and“Internet Biophotonics.”All eight papers in this special issue are research papers.

关键词： Junior photonics Russia

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ASSESSMENT OF TISSUE OPTICAL CLEARING AS A FUNCTION OF GLUCOSE CONCENTRATION USING OPTICAL COHERENCE TOMOGRAPHY

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Journal of Innovative Optical Health Sciences 2010年第3期3卷 169-176页

作者： NARENDRAN SUDHEENDRAN MOHAMED MOHAMED MOHAMAD G.GHOSN vALERY v.TUCHIN kirill v.LARIN Department of Electrical and Computer Engineering University of Houston N308 Engineering Building 1 HoustonTX 77204USA Department of Biomedical Engineering University of Houston 2028 SERC Building HoustonTX 77204USA Department of Medicine Baylor College of Medicine HoustonTX 77030USA Institute of Optics and Biophotonics Saratov State University Saratov 410012Russia Institute of Precise Mechanics and Control of RAS Saratov 410056 Russia

One of the major challenges in imaging biological tissues using optical techniques,such as optical coherence tomography(OCT),is the lack of light penetration due to highly turbid structures within the *** clearing techniques enable the biological samples to be more optically homogeneous,allowing for deeper penetration of light into the *** study investigates the effect of optical clearing utilizing various concentrations of glucose solution(10%,30%,and 50%)on porcine skin.A gold-plated mirror was imaged beneath the tissue and percentage clearing was determined by monitoring the change in reflected light intensity from the mirror over *** ratio of percentage clearing per tissue thickness for 10%,30% and 50% glucose was determined to be 4.7±1.6%mm^(−1)(n=6),10.6±2.0%mm^(−1)(n=7)and 21.8±2.2%mm^(−1)(n=5),*** was concluded that while higher glucose concentration has the highest optical clearing effect,a suitable concentration should be chosen for the purpose of clearing,considering the osmotic stress on the tissue sample.

关键词： Glucose porcine skin percent clearing scattering coefficient optical coherence tomography

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Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations

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Nano-Micro Letters 2021年第8期13卷 263-280页

作者： valery v.Prokhorov Nikolay A.Barinov kirill A.Prusakov Evgeniy v.Dubrovin Maxim D.Frank-Kamenetskii Dmitry v.Klinov Federal Research and Clinical Center of Physical-Chemical Medicine Malaya Pirogovskaya1aMoscow 119435Russian Federation A.N.Frumkin Institute of Physical Chemistry and Electrochemistry RASLeninsky prospect Moscow 199071 Russian Federation 3 Moscow Institute of Physics and TechnologyInstitutskiy per.9Dolgoprudny141700 MoscowRussian Federation Lomonosov Moscow State University Leninskie gory1-2Moscow 119991Russian Federation Department of Biomedical Engineering Boston University44 Cummington MallBoston MA02215USA

Up to now,the DNA molecule adsorbed on a surface was believed to always preserve its native *** belief implies a negligible contribution of lateral surface forces during and after DNA adsorption although their impact has never been ***-resolution atomic force microscopy was used to observe that stiff DNA molecules kinetically trapped on monomolecular films comprising one-dimensional periodically charged lamellar templates as a single layer or as a sublayer are oversaturated by sharp discontinuous kinks and can also be locally melted and *** argue that kink/anti-kink pairs are induced by an overcritical lateral bending stress(>30 pNnm)inevitable for the highly anisotropic 1D-1D electrostatic interaction of DNA and underlying rows of positive surface *** addition,the unexpected kink-inducing mechanical instability in the shape of the template-directed DNA confined between the positively charged lamellar sides is observed indicating the strong impact of *** previously reported anomalously low values of the persistence length of the surface-adsorbed DNA are explained by the impact of the surface-induced low-scale *** sites of the local melting and supercoiling are convincingly introduced as other lateral stress-induced structural DNA anomalies by establishing a link with DNA high-force *** results open up the study in the completely unexplored area of the principally anomalous kinetically trapped DNA surface conformations in which the DNA local mechanical response to the surface-induced spatially modulated lateral electrostatic stress is essentially *** underlying rich and complex in-plane nonlinear physics acts at the nanoscale beyond the scope of applicability of the worm-like chain approximation.

关键词： DNA surface conformations Kinetic trapping Lateral stress Periodically charged surface DNA kinks

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Modeling of cold-temperate tree Pinus koraiensis (Pinaceae) distribution in the Asia-Pacific region: Climate change impact

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Forest Ecosystems 2022年第2期9卷 160-167页

作者： Tatyana Y.Petrenko kirill A.Korznikov Dmitry E.Kislov Nadezhda G.Belyaeva Pavel v.Krestov Botanical Garden-Institute FEB RAS Makovskogo St.142Vladivostok690024Russia Institute of Geography RAS Staromonetniy 24-4Moscow119017Russia

Background:Pinus koraiensis Siebold&Zucc.(Korean pine)is a key species of the mixed cold temperate forests of Northeast *** climate change can significantly worsen the quality of *** habitats and therefore lead to a large-scale structural and functional transformation of the East Asian mixed *** built a species distribution model(SDM)for *** using the random forest classifier–a versatile machine learning al-gorithm,to discover overlap areas of potential species occurrence in the climate condition of the Last Glacial Maximum(~21,000 year before present)and in the projected future climates(2070 year),from which possible permanent refugia for *** were ***:Using the random forest supervised learning algorithm,we developed models of the modern distribution of *** in accordance with the five selected bioclimatic variables(Kira’s warmth and coldness indices,the index of continentality,the rain precipitation index,and the snow precipitation index).In addition to current climatic conditions,we performed this analysis for the climate of the Last Glacial Maximum and for the future projected climate(2070)under scenarios RCP2.6 and *** the predictors,the rain index appears to be the most *** land area estimates with high suitability for *** was 303,785 km 2 under current climatic conditions,586,499 km 2 for the Last Glacial Maximum,and 337,573 km^(2) for the future(2070)period under the RCP2.6 scenario,and 397,764 km^(2) under the RCP8.5 ***:Most of the potential range of *** during the Last Glacial Maximum was located outside the current distribution area of the *** climatically suitable *** habitats will likely disappear in the western part of its modern *** the southern part of the range,which includes glacial refugia,the areas of continuous distribution of the *** populations since the end of the Pleistocene are expected to

关键词： Climate change Bioclimatic modeling Species distribution model Korean pine Northeast Asia

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Improvement of tissue analysis and classification using optical coherence tomography combined with Raman spectroscopy

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Journal of Innovative Optical Health Sciences 2015年第4期8卷 10-19页

作者： Chih-Hao Liu Ji Qi Jing Lu Shang Wang Chen Wu Wei-Chuan Shih kirill v.Larin Department of Biomedical Engineering University of Houston 3605 Cullen Blvd. HoustonTexas 77204-5060USA Department of Electrical and Computer Engineering University of Houston 4800 Calhoun Rd. HoustonTexas 77204USA Department of Molecular Physiology and Biophysics Baylor College of Medicine One Baylor Plaza HoustonTexas 77030USA

Optical coherence tomography(OCT)provides significant advantages of high resolution(approaching the histopathology level)realtime imaging of tsess without use of contrast *** on these advantages,the microstructural features of tumors can be visualized and detected ***,it is still not clinically accepted for tumor margin delin-eation due to poor specificity and *** contrast,Raman spectroscopy(RS)can obtain tissue information at the molecular level,but does not provide real-time inaging ***,combining OCT and RS could provide *** this end,we present a tissue analysis and dassification method using both the slope of OCT intensity signal vs depth and the principle components from the RS spectrum as the indicators for tissuse *** goal of this study was to understand prediction accuracy of OCT and combined OCT/RS method for dassification of optically similar tisues and *** pilot experiments were performed on mouse kidneys,livers,and small intestines(SIs).The prediction accuracy with five-fold cross validation of the method has been evaluated by the support vector machine(SvM)*** results demonstrate that tissue characterization based on the OCT/RS method was superior compared to using OCT structural information *** combined OCT/RS method is potentially useful as a noninvasive optical biopsy technique for rapid and automatic tissue characterization during surgery.

关键词： OCT signal slope principle component analysis multi-support vector machine Raman spectra

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