Article
Plant Sciences
Narcis Ferrer-Ledo, Lars Stegemueller, Marcel Janssen, Rene H. Wijffels, Maria J. Barbosa
Summary: Temperature is an important environmental parameter in outdoors cultivation of microalgae. It has a significant impact on growth, photosynthesis, and lipid accumulation. Lower temperatures increase fatty acid desaturation, while higher temperatures have the opposite effect.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Mechanics
Riccardo Marcaccioli, Jean-Philippe Bouchaud, Michael Benzaquen
Summary: By synchronizing a database of stock specific news with 5 years worth of order book data on 300 stocks, the study examines the different dynamical features of abnormal price movements following news releases and those arising spontaneously. The research finds that large volatility fluctuations induced by exogenous events occur abruptly and are followed by a decaying power-law relaxation, while endogenous price jumps are characterized by progressively accelerating growth of volatility, also followed by a power-law relaxation, but slower than for exogenous jumps. These findings are reminiscent of observations in other contexts such as Amazon book sales and YouTube views.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Agriculture, Dairy & Animal Science
M. N. Engelsmann, L. D. Jensen, M. E. van der Heide, M. S. Hedemann, T. S. Nielsen, J. Norgaard
Summary: This study evaluated the digestibility of protein and amino acids from different protein sources and the intestinal morphology in pigs during the first four weeks after weaning. The results showed that the time after weaning was more important for protein digestibility than the source of protein. The lower number of mature epithelial cells and smaller absorptive area in the small intestine during the early postweaning period may explain the poor protein digestibility.
Article
Engineering, Environmental
Chen Cai, Yu Hua, Huiling Liu, Xiaohu Dai
Summary: This study demonstrates the potential of recycling cephalosporin fermentation residue (CFR) into plant biostimulants through partial acid hydrolysis. Two favorable hydrolysis conditions were identified, resulting in biostimulants with plant growth promotion and stress alleviation properties. The biostimulants derived from CFR showed differences in aminograms and profiles of low molecular weight compounds, indicating potential variability in their effects on plants.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Chemistry, Applied
Dezhi Yuan, Hua Lv, Tiantian Wang, Yulu Rao, Yibo Tang, Yiwen Chu, Xinrong Wang, Jiafu Lin, Peng Gao, Tao Song
Summary: This study reports the discovery of a novel alpha-agarase, AgaB, with an N-terminal CBM2 domain. AgaB exhibited activity against agarose and produced agarotetraose and agarohexaose. The study also found that CBM2 aids in substrate binding and identified possible catalytic amino acids, E468 and D333.
Article
Plant Sciences
Julien Besnard, Unnati Sonawala, Bal Maharjan, Eva Collakova, Scott A. Finlayson, Guillaume Pilot, John McDowell, Sakiko Okumoto
Summary: Amino acids play important roles in biosynthesis and signaling, affecting plant development and immune responses. Changes in amino acid levels can trigger stress phenotypes and pathogen resistance through various pathways, indicating a link between amino acid transport and stress responses.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Physics, Applied
L. Han, X. Z. Chen, X. L. Li, J. Zhang, J. F. Feng, F. Li, C. Song, F. Pan
Summary: The study investigates the bias-dependent tunneling anisotropic magnetoresistance effect in antiferromagnetic materials, which shows polarity reversal with increasing bias voltage. This effect can be explained by first-principles calculations, revealing a unique crossing point and subsequent magnitude reversal between the antiferromagnetic and ferromagnetic phases. Harnessing tunneling behavior through feasible bias voltage in antiferromagnetic-based junctions is a promising frontier in antiferromagnet spintronics.
APPLIED PHYSICS LETTERS
(2021)
Article
Multidisciplinary Sciences
Chia-Ru Chung, Jhen-Ting Liou, Li-Ching Wu, Jorng-Tzong Horng, Tzong-Yi Lee
Summary: This study used multi-label classifiers and algorithm adaptation techniques to predict different functions of antimicrobial peptides (AMPs) in various pathogens. The study found that sequence order and charge were critical, and specific amino acids (C and E) were discriminative. These findings provide valuable insights for designing multi-functional AMPs to combat drug-resistant pathogens.
Article
Nutrition & Dietetics
Berenice Palacios-Gonzalez, Guadalupe Leon-Reyes, Berenice Rivera-Paredez, Isabel Ibarra-Gonzalez, Marcela Vela-Amieva, Yvonne N. Flores, Samuel Canizales-Quinteros, Jorge Salmeron, Rafael Velazquez-Cruz
Summary: This study aims to investigate the sex-specific serum modifications of amino acids and acylcarnitines (ACs) and their relationship with MetS in the Mexican population. The findings show that a serum amino acid signature (citrulline and glycine) and medium-chain ACs (AC14:1, AC10, and AC18:10H) are associated with MetS. Glycine and AC10 are specific metabolites for discrimination based on sex-dependent MetS. Additionally, glycine and short-chain ACs (AC2, AC3, and AC8:1) are associated with age-dependent MetS.
Article
Biochemistry & Molecular Biology
Guofeng Bao, Liqiang Mu, Ying Wang
Summary: The effect of growth temperature on the nutritional components and metabolites of wild soybean was studied using gas chromatography-time-of-flight mass spectrometry (GC-TOF-MS). A total of 430 metabolites were identified and analyzed, and 87 metabolites significantly differed in the sixth accumulated temperature region compared to the other regions. Amino acid metabolism was found to have the greatest influence on wild soybean quality.
Article
Agronomy
Kaidi Cui, Lin Zhou, Chaofan Jiang, Song Yang, Nan Zou, Feng Liu, Leiming He, Wei Mu
Summary: This study investigated the insecticidal efficacy, accumulation, and dissipation of benzothiazole in grains (wheat, corn, and rice) under different temperatures. A universal detection method was established for benzothiazole residues in three grains. The results showed that the insecticidal efficacy and accumulation/dissipation rate of benzothiazole were influenced by temperature. Corn had the highest insecticidal efficacy, while rice had the highest accumulation and dissipation rate. These findings provide important references for the application of benzothiazole and other fumigants.
PEST MANAGEMENT SCIENCE
(2023)
Article
Polymer Science
Rini Sharma, Natrajan Vijay, Beom Jin Kim, Hyung-il Lee
Summary: In this study, a novel fluorescent copolymer with solvatochromic and aggregation-induced emissive properties was introduced. It demonstrated significant fluorescence in nonpolar solvents and increased fluorescence intensity with increasing temperature in aqueous solution. The copolymer holds promise for temperature sensing in biological systems and bioimaging.
EUROPEAN POLYMER JOURNAL
(2023)
Article
Multidisciplinary Sciences
Diego del Alamo, Lillian DeSousa, Rahul M. Nair, Suhaila Rahman, Jens Meiler, Hassane S. Mchaourab
Summary: The APC transporter GadC plays a role in the survival of pathogenic bacteria under extreme acid stress. Through studying its conformational dynamics using DEER spectroscopy, researchers discovered acid-induced conformational changes in GadC, enabling isomerization between inward- and outward-facing states. The substrate glutamate modulates the dynamics of an extracellular gate. This study provides insights into the conformational cycle of GadC and highlights the divergence in dynamics among different families in the LeuT-fold.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Ana R. Rebelo, Catarina C. F. Homem
Summary: Tumor cells have an increased demand for nutrients, and the role of plasma membrane metabolic transporters in tumor growth has been analyzed in Drosophila brain tumors. It was found that 13 plasma membrane metabolic transporters are upregulated in tumors and required for tumor growth. CD98hc and several light chains were identified as crucial players in tumor progression by forming heterodimeric amino acid transporters.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Hiep T. Dao, Nishchal K. Sharma, Emma J. Bradbury, Robert A. Swick
Summary: This study showed that supplementing Arg or Cit to Arg-deficient diets for broilers can improve body weight gain and reduce feed conversion ratio. Adding GAA to the diets had a lowering effect on feed conversion ratio, but did not significantly increase body weight gain.
JOURNAL OF ANIMAL PHYSIOLOGY AND ANIMAL NUTRITION
(2021)
Article
Multidisciplinary Sciences
Shristi Pawnikar, Brenda S. Magenheimer, Ericka Nevarez Munoz, Robin L. Maser, Yinglong Miao
Summary: This study combines experimental and computational methods to elucidate the activation mechanism of Polycystin-1 (PC1), which is crucial for future drug design targeting PC1.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Matthew M. Copeland, Hung N. Do, Lane Votapka, Keya Joshi, Jinan Wang, Rommie E. Amaro, Yinglong Miao
Summary: GaMD is a computational technique that provides enhanced sampling and free energy calculations for biomolecules, and its implementation in OpenMM has been validated on model systems of alanine dipeptide and RNA folding.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Viswanathan Gurumoorthy, Utsab R. Shrestha, Qiu Zhang, Sai Venkatesh Pingali, Eric T. Boder, Volker S. Urban, Jeremy C. Smith, Loukas Petridis, Hugh O'Neill
Summary: c-Src kinase is a non-receptor tyrosine kinase that phosphorylates signaling proteins in cancers. This study focuses on the N-terminal disordered region (SH4UD) and its interactions with other domains of c-Src kinase. The results show that the presence of SH4UD leads to structural changes in the regulatory domains (SH3-SH2), indicating the importance of the disordered region for allosteric interactions. This study provides insights that may aid in the development of therapeutic interventions targeting the regulatory domains of c-Src kinase.
Article
Chemistry, Physical
Jinan Wang, Yinglong Miao
Summary: This study presents LiGaMD2, an improved method for sampling ligand binding and dissociation by applying a selective boost potential to both the ligand and protein residues in the binding pocket. LiGaMD2 efficiently captured repetitive ligand dissociation and binding in microsecond simulations and produced accurate ligand binding kinetics and free energy values. Therefore, LiGaMD2 provides an efficient approach for calculating ligand binding thermodynamics and kinetics.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Luoxi Tan, Haden L. Scott, Micholas Dean Smith, Sai Venkatesh Pingali, Hugh M. O'Neill, Jennifer L. Morrell-Falvey, John Katsaras, Jeremy C. Smith, Brian H. Davison, James G. Elkins, Jonathan D. Nickels
Summary: Biofuels are crucial for sustainable energy and optimizing their production is a societal and economic imperative. Reducing the toxicity of co-solvents can improve the efficiency of biofuel production.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Physical
Mood Mohan, Micholas Dean Smith, Omar Demerdash, Michelle K. Kidder, Jeremy C. Smith
Summary: Understanding the physical properties of ionic liquids is crucial for various industrial and research applications, but experimental screening can be challenging and expensive. Previous research has shown that combining quantum-mechanics-based property prediction tools with machine learning approaches can help screen and design ionic liquids with desired properties. However, the most appropriate machine learning approach is still unclear.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Review
Chemistry, Physical
Jinan Wang, Hung N. Do, Kushal Koirala, Yinglong Miao
Summary: Biomolecular binding kinetics, including association and dissociation rates, are crucial for the design of therapeutic drugs. The drug molecule's residence time or dissociation rate has shown a better correlation with efficacy compared to binding affinities. Various modeling approaches, such as structure-kinetic relationship models, molecular dynamics simulations, enhanced sampling, and machine learning, have been developed to explore biomolecular binding mechanisms and predict binding rates. In this review, we discuss recent advancements in computational modeling of biomolecular binding kinetics and the potential for future improvements.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Hung N. Do, Yinglong Miao
Summary: We have developed a new deep boosted molecular dynamics (DBMD) method that uses probabilistic Bayesian neural network models to construct boost potentials for accurate energetic reweighting and enhanced sampling of molecular simulations. The DBMD method was successfully applied to alanine dipeptide, fast-folding proteins, and RNA structures, achieving improved sampling and reproducing accurate free energy profiles. DBMD also showed the capability to capture folding pathways and identify low-energy conformations in simulations of protein and RNA systems.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Shristi Pawnikar, Apurba Bhattarai, S. Xiaohu Ouyang, Ramir Vega, Yuan Chen, Yinglong Miao
Summary: Post-translational modifications by small ubiquitin-like modifiers (SUMOs) are dysregulated in many types of cancers. The SUMO E1 enzyme has recently been suggested as a new immuno-oncology target. COH000 was identified as an allosteric covalent inhibitor of SUMO E1, but there were inconsistencies between its X-ray structure and the structure-activity relationship (SAR) data of inhibitor analogues. By conducting Ligand Gaussian accelerated molecular dynamics (LiGaMD) simulations, we uncovered a critical non-covalent binding intermediate of COH000 that agreed well with published and new SAR data, resolving the discrepancy.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Multidisciplinary Sciences
Yanyan Xue, Jun Li, Dian Chen, Xizhu Zhao, Liang Hong, Yu Liu
Summary: This study develops a method to monitor the conformational change of riboSAM during transcription, and observes five co-existing states in riboSAM. A bifurcated helix structure is identified in one of the states and is found to be responsible for translation inhibition. This strategy enables the precise mapping of RNA conformational landscape during transcription.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Mood Mohan, Micholas Dean Smith, Omar N. Demerdash, Blake A. Simmons, Seema Singh, Michelle K. Kidder, Jeremy C. Smith
Summary: Ionic liquids (ILs) have unique solvent properties, but it is unrealistic to experimentally determine their physicochemical properties. To address this issue, we developed machine learning models to predict the surface tension and speed of sound of ILs, which showed excellent agreement with experimental observations. This study paves the way for the development of machine learning models for predicting IL properties.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Physical
Shristi Pawnikar, Apurba Bhattarai, S. Xiaohu Ouyang, Ramir Vega, Yuan Chen, Yinglong Miao
Summary: Through novel Ligand Gaussian accelerated molecular dynamics (LiGaMD) simulations, we have identified a critical low-energy non-covalent binding intermediate conformation of COH000 that agrees excellently with published and new structure-activity relationship (SAR) data of COH000 analogues, which are inconsistent with the X-ray structure. Our biochemical experiments and LiGaMD simulations have uncovered a critical non-covalent binding intermediate during allosteric inhibition of the SUMO E1 complex.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Medicinal
Rupesh Agarwal, T. Rajitha Rajeshwar, Jeremy C. Smith
Summary: Structure-based virtual high-throughput screening is commonly used in early-stage drug discovery. This study evaluated the performance of three docking protocols on 173 RNA-small molecule crystal structures. The results showed that Vina and rDock are both applicable for projects without known ligand-protein structures, but their performance is relatively poor compared to protein-target docking methods.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Jun Li, JingFei Xie, Aljaz Godec, Keith R. Weninger, Cong Liu, Jeremy C. Smith, Liang Hong
Summary: By conducting experiments and simulations, we have discovered that the inter-domain motion of protein molecules does not exhibit ergodicity in certain time ranges, unlike the ergodic behavior of DNA. This suggests that seemingly identical protein molecules can have dynamic and functional differences.
Article
Biochemistry & Molecular Biology
Jinan Wang, Lan Lan, Xiaoqing Wu, Liang Xu, Yinglong Miao
Summary: The Musashi RNA-binding proteins play important roles in regulating mRNA translation, cell stemness, and tumorigenesis. Musashi-1 (MSI1), previously known as an intestinal and neural stem cell marker, has been found to be overexpressed in many cancers and is a significant drug target for acute myeloid leukemia and solid tumors. In this study, researchers utilized all-atom microsecond-timescale simulations to investigate the dynamic mechanism of Numb RNA binding to MSI1. Their simulations revealed important intermediate conformational states during RNA binding and provide insight for structure-based drug design targeting MSI1 and other RBPs.
CURRENT RESEARCH IN STRUCTURAL BIOLOGY
(2022)