Article
Biochemistry & Molecular Biology
Siddhant Chaturvedi, Neha Thakur, Shahirina Khan, Mithilesh Kumar Sardar, Alka Jangra, Siddharth Tiwari
Summary: In this study, the banana cultivar Nendran was found to have the highest concentration of ascorbic acid (AsA). Five genes related to AsA synthesis were identified from the banana genome database, and three of them were shown to significantly enhance AsA levels in plant leaves through overexpression in Arabidopsis thaliana. The findings of this study have important implications for the development of AsA-rich plants, particularly in developing countries where staple foods are crucial.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Natalia Hess, Simon Richter, Michael Liebthal, Karl-Josef Dietz, Angelika Mustroph
Summary: The chloroplast primary metabolism is tightly regulated to respond to various environmental conditions, including daily changes between day and night. Thioredoxin-mediated redox regulation is a crucial component in regulating plastid-localized metabolic enzymes, ensuring proper assimilation and dissimilation processes in plants.
Article
Plant Sciences
Nazish Annum, Moddassir Ahmed, Mark Tester, Zahid Mukhtar, Nasir Ahmad Saeed
Summary: This study investigated the role of Phospholipase C Isoform 5 (PLC5) in thermotolerance in Arabidopsis thaliana. The results showed that over-expression of PLC5 contributes to heat stress tolerance and maintains photosynthetic activity, with effects on root development.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Naia P. Santos, Wai Tuck Soh, Fatih Demir, Raimund Tenhaken, Peter Briza, Pitter F. Huesgen, Hans Brandstetter, Elfriede Dall
Summary: In this study, we identified AtCYT beta as a natural inhibitor of legumain isoform b (AtLEGb) in Arabidopsis thaliana, through pull-down experiments. Biochemical analysis revealed that AtCYT beta inhibits both AtLEG beta and papain-like cysteine proteases via two separate cystatin domains. The interaction between AtCYT beta and legumain is facilitated by a conserved asparagine residue and stabilized by charged exosite interactions, leading to pH-dependent inhibition. The findings suggest a context-specific regulatory mechanism of AtLEGb with implications for plant physiology and programmed cell death.
Article
Plant Sciences
Wei Wang, Sonja Viljamaa, Ondrej Hodek, Thomas Moritz, Totte Niittyla
Summary: The role of SUS in cellulose biosynthesis in Arabidopsis has been refuted, as alternative UDP-glucose biosynthesis pathways were found to be employed.
Article
Plant Sciences
Marc Somssich, Filip Vandenbussche, Alexander Ivakov, Norma Funke, Colin Ruprecht, Kris Vissenberg, Dominique Van Der Straeten, Staffan Persson, Dmitry Suslov
Summary: This study investigated the effects of brassinosteroids on Arabidopsis hypocotyl growth responses to gravity, revealing the importance of changes in cellulose and mannan content in regulating plant gravitropic bending and upright posture. It was found that brassinosteroids interfere with plant growth by affecting cellulose fibre organization and cell expansion, as well as by influencing the presence of mannans in the cell walls.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Pinky Dhatterwal, Sandhya Mehrotra, Anthony J. Miller, Raviprasad Aduri, Rajesh Mehrotra
Summary: The study reveals the induction of AtAVT6D in response to ABA and osmotic stress. AtAVT6D is localized to the plasma membrane and involved in Aspartic acid uptake. The Pro.C2 promoter of AtAVT6D can be used as a stress-inducible promoter to drive transgene expression.
PLANT MOLECULAR BIOLOGY
(2022)
Review
Chemistry, Applied
Holly Allen, Donghui Wei, Ying Gu, Shundai Li
Summary: This review summarizes the major hypotheses and advancements made in the past century regarding the regulation of cellulose biosynthesis, with a focus on Arabidopsis thaliana.
CARBOHYDRATE POLYMERS
(2021)
Article
Plant Sciences
Joanna M. Chustecki, Ross D. Etherington, Daniel J. Gibbs, Iain G. Johnston
Summary: This study shows that plant mitochondria move to facilitate potential exchange between organelles, and that this movement is influenced by genetic and physical factors. The altered mitochondrial dynamics observed in the msh1 mutant suggest a compensatory mechanism for maintaining genetic structure.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemical Research Methods
Guoxian Yu, Qiuyue Huang, Xiangliang Zhang, Maozu Guo, Jun Wang
Summary: Alternative splicing allows a gene to produce multiple isoforms, and predicting the functions of these isoforms is crucial for understanding protein functional diversity. Existing methods fail to consider the tissue specificity of alternative splicing, while our proposed TS-Isofun integrates multiple functional association networks to predict isoform functions and optimizes the weights and predictions together.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Ivano Forgione, Antonella Muto, Magdalena Woloszynska, Adriana Ada Chiappetta, Michele Ferrari, Mieke Van Lijsebettens, Maria Beatrice Bitonti, Leonardo Bruno
Summary: This study explores the molecular basis of the abnormal leaf phenotype in the ddc mutant of Arabidopsis thaliana. It demonstrates that misexpression of genes related to leaf fate commitment and morphogenesis, such as CLF and KNAT6, is responsible for the abnormal phenotype. Epigenetic mechanisms, including DNA methylation and histone modifications, are proposed to regulate the expression of these genes during leaf morphogenesis in the ddc mutant.
Article
Plant Sciences
Alvin Sanjaya, Yusuke Kazama, Kotaro Ishii, Ryohsuke Muramatsu, Kengo Kanamaru, Sumie Ohbu, Tomoko Abe, Makoto T. Fujiwara
Summary: Argon-ion beam mutagenesis induced a pale green mutant of Arabidopsis thaliana, named Ar50-33-pg1, with significant shrinkage of mesophyll chloroplasts during the chlorotic process. Genetic analysis revealed a large deletion in chromosome V, including the EGY1 gene, which was found to be responsible for the pale phenotype. Ultrastructural analysis showed disassembled chloroplasts in Ar50-33-pg1 and egy1, indicating the crucial role of EGY1 in chloroplast maintenance.
Article
Plant Sciences
Mei Bai, Han Gao, Yang Yang, Hong Wu
Summary: In mature pollen grains, lipids are primarily stored in lipid droplets and play a crucial role in pollen development and germination. The enzyme DGAT1 is important for triacylglycerol synthesis and its mutation leads to a decrease in TAG content and altered fatty acid composition in pollen. The expression of genes involved in TAG synthesis is downregulated in the mutant pollen as11, while starch synthesis genes are upregulated. The mutant pollen also exhibits changes in lipid droplet content and ultrastructural alterations, including a decrease in endoplasmic reticulum and increase in Golgi body content.
Article
Plant Sciences
Aakanksha Singh, Julia Compart, Shadha Abduljaleel AL-Rawi, Harendra Mahto, Abubakar Musa Ahmad, Joerg Fettke
Summary: The non-catalytic starch-binding proteins LESV and ESV1 play a crucial role in starch metabolism, affecting phosphorylation, hydrolysis and synthesis processes. They also induce stable alterations in the glucan structures at the surface of starch granules.
Article
Biochemistry & Molecular Biology
Yonghui Dong, Liron Feldberg, Ilana Rogachev, Asaph Aharoni
Summary: Stable isotope labeling using DLEMMA was used to identify and track the phenylpropanoid pathway in Arabidopsis thaliana, resulting in the discovery of 35 phenylalanine-derived metabolites. A comparison between wild type and mutant leaves revealed 30 differential metabolites, with ectopic PAP1 expression leading to significant changes in anthocyanins and flavonols accumulation.
Article
Chemistry, Multidisciplinary
Benjamin P. Allen, Zoe M. Wright, Hailey F. Taylor, Thomas J. Oweida, Sabila Kader-Pinky, Emily F. Patteson, Kara M. Bucci, Caleb A. Cox, Abishec Sundar Senthilvel, Yaroslava G. Yingling, Abigail S. Knight
Summary: This study presents a systematic investigation of the structure-assembly relationships of peptide-polymer amphiphiles (PPAs). The study reveals that the molecular weight and hydrophilicity of the oligomer control the morphology of the PPAs, while the dispersity and charge density of the peptide affect the particle size. These findings provide important benchmarks for the rational design of PPAs with enhanced biomimetic functionality.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Physical
Akhlak U. Mahmood, Yaroslava G. Yingling
Summary: Magnetic nanoparticles (MNPs) can self-assemble into ordered structures with unique geometries. A new atomistic molecular dynamics simulation method is proposed to study the dynamics, self-assembly, structure, and properties of MNPs under different core sizes and shapes, ligand chemistry, solvent properties, and external fields. The simulation of oleic acid ligand-functionalized magnetite (Fe3O4) nanoparticles shows that electrostatic interactions favor the formation of chains over rings, ligands promote cluster growth, and solvents reduce rotational diffusion. The parallelized algorithm can be used as a plugin for LAMMPS to gain insights into the physics and chemistry of magnetic assembly processes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Plant Sciences
Daniel Restrepo-Montoya, Amanda M. Hulse-Kemp, Jodi A. Scheffler, Candace H. Haigler, Lori L. Hinze, Janna Love, Richard G. Percy, Don C. Jones, James Frelichowski
Summary: This research analyzed the standardized cotton traits within the National Cotton Germplasm Collection and found significant associations between different groups, providing valuable information for further research and breeding.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Juan Du, Venu Gopal Vandavasi, Kelly R. Molloy, Hui Yang, Lynnicia N. Massenburg, Abhishek Singh, Albert L. Kwansa, Yaroslava G. Yingling, Hugh O'Neill, Brian T. Chait, Manish Kumar, B. Tracy Nixon
Summary: Higher plants use membrane-bound cellulose synthase complexes to synthesize cellulose, with homomeric trimers possibly playing an important role in cell wall synthesis, and key residues for future studies have been identified.
Article
Biophysics
Jessica A. Nash, Matthew D. Manning, Alexey V. Gulyuk, Aleksey E. Kuznetsov, Yaroslava G. Yingling
Summary: RNA-based therapeutics have great potential in treating various diseases. This study used simulations to investigate the ability of cationic ligand functionalized gold nanoparticles to bend dsRNA and designed nanoparticles with controlled internal binding to RNA's major groove. The findings have important implications in packaging nucleic acids for nanotechnology and gene delivery.
Article
Chemistry, Physical
Sabila K. Pinky, Albert L. Kwansa, Buang Zhang, Adrienne D. Stiff-Roberts, Yaroslava G. Yingling
Summary: The morphology of conjugated polymer thin films is influenced by the emulsion characteristics, but the understanding of how these characteristics control the film properties and device performance is still unclear. In this study, molecular dynamics simulations were conducted on emulsions containing polyfluorene (PFO) polymer and various solvents to investigate the relationship between emulsion properties and the morphology of deposited PFO thin films. The results showed that a primary solvent with low solubility-in-water and high non-bonded interaction energy ratio among the solvent, polymer, and water produced smoother and denser films.
Article
Materials Science, Biomaterials
Atrouli Chatterjee, Preeta Pratakshya, Albert L. Kwansa, Nikhil Kaimal, Andrew H. Cannon, Barbara Sartori, Benedetta Marmiroli, Helen Orins, Zhijing Feng, Samantha Drake, Justin Couvrette, LeAnn Le, Sigrid Bernstorff, Yaroslava G. Yingling, Alon A. Gorodetsky
Summary: By combining experimental and computational methods, we systematically mapped the three-dimensional refractive index distributions of model self-assembled reflectin-based structures, which can improve understanding of squid skin cell functionality and enhance characterization of protein-based optical materials.
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2023)
Article
Nanoscience & Nanotechnology
Buang Zhang, Sabila K. Pinky, Albert L. Kwansa, Spencer Ferguson, Yaroslava G. Yingling, Adrienne D. Stiff-Roberts
Summary: Thin films of polyfluorene (PFO) were successfully deposited using the emulsion based resonant infrared, matrix-assisted pulsed laser evaporation (RIR-MAPLE) method. It was found that the selection of surfactant can increase the crystalline-fi phase content and improve the color purity of light emission. Comparison of blue light-emitting diodes (LEDs) with different surfactants showed the significant impact of surfactant on device performance.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Akhlak U. Mahmood, Mehedi H. Rizvi, Joseph B. Tracy, Yaroslava G. Yingling
Summary: Inorganic colloidal nanoparticle (NP) properties can be controlled by stripping stabilizing ligands using a poor solvent. This study investigates the stripping process of oleylamine ligands from magnetite (Fe3O4) NPs in different ethanol/hexane mixtures. The results reveal the complex interactions between ethanol and system components, and suggest the existence of a threshold concentration of ethanol for effective ligand stripping. The study provides insights into the ligand-solvent interactions and offers a computational approach for studying ligand stripping from colloidal NPs.
Article
Polymer Science
Albert L. L. Kwansa, Rakhee C. C. Pani, Joseph A. A. DeLoach, Arianna Tieppo, Eric J. J. Moskala, Steven T. T. Perri, Yaroslava G. G. Yingling
Summary: Plasticizers improve the flexibility and durability of polymer materials by reducing glass transition and cold flex temperatures. However, the migration and exudation of plasticizers from polymer materials have hindered the development of efficient and safe plasticizers. This study used molecular dynamics simulations validated by experiment to investigate the molecular mechanism of exudation of different plasticizers from PVC, and found that plasticizer-PVC compatibility was the main determinant of exudation.
Article
Chemistry, Physical
Juseok Choi, Albert L. Kwansa, Yaroslava G. Yingling, Seong H. Kim
Summary: Vibrational sum frequency generation (SFG) spectroscopy is commonly used to analyze the structural information of molecular functional groups at two-dimensional interfaces in gas or liquid mediums. However, interpreting the measured intensity in terms of molecular orientation with respect to laboratory coordinates is challenging. This study utilized density functional theory to calculate the polarizability and dipole derivative tensors of different molecules, allowing for the theoretical calculation of their SFG intensities in relation to the tilt angle of the CH3 group with respect to the surface normal direction. The findings suggest that the vibrational coupling among neighboring functional groups is significant and should not be ignored in SFG experiments.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemistry & Molecular Biology
Preeti Verma, Albert L. Kwansa, Ruoya Ho, Yaroslava G. Yingling, Jochen Zimmer
Summary: Cellulose, a major component of plant cell walls, is synthesized by cellulose synthase through translocation. In this study, cryogenic electron microscopy structures of the substrate and product bound to cellulose synthase isoform-8 from aspen were presented. UDP-glucose binds to a catalytic pocket adjacent to a transmembrane channel, and the glucosyl unit of the substrate is coordinated by conserved residues and amphipathic interface helices. Mutagenesis of a conserved gating loop revealed its critical role in catalytic activity. Molecular dynamics simulations showed prolonged interactions between the gating loop and the substrate, facilitating proper positioning for glycosyl transfer and cellulose translocation.
Article
Multidisciplinary Sciences
Thomas J. Oweida, Yaroslava G. Yingling
Summary: This study presents a method that integrates experimental small-angle X-ray scattering data and all-atom molecular modeling data using a genetic algorithm method for the determination of the atomistic representation of poly-Thymine DNA in solution. The results validate the performance of various AMBER force fields and implicit solvent models for ssDNA and enable a better understanding of the behavior of ssDNA in solution.
ADVANCED THEORY AND SIMULATIONS
(2023)
Article
Environmental Sciences
James S. Peerless, Alexey Gulyuk, Nina J. B. Milliken, Gyu Dong Kim, Elliot Reid, Jae Woo Lee, Dooil Kim, Zachary Hendren, Young Chul Choi, Yaroslava G. Yingling
Summary: Brine desalination is important for reducing the environmental impact of contaminated wastewater, but current techniques require high energy. We tested 10 organic solvents for solvent-based desalination efficacy using experiments and simulations. Solvents that form partial nanoscale phases effectively remove salt ions and capture water molecules. Our results contribute to the rational design of solvents for efficient desalination and low-cost fresh water production.
Article
Chemistry, Multidisciplinary
Benjamin P. Allen, Zoe M. Wright, Hailey F. Taylor, Thomas J. Oweida, Sabila Kader-Pinky, Emily F. Patteson, Kara M. Bucci, Caleb A. Cox, Abishec Sundar Senthilvel, Yaroslava G. Yingling, Abigail S. Knight
Summary: This study systematically investigates the structure-assembly relationships of PPAs, revealing that oligomer molecular weight and peptide hydrophilicity dictate morphology, while dispersity and peptide charge affect particle size.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)