Article
Agronomy
Di Zhou, Jia-Ling Zhao, Rui Wang, Hai-Lin Wang, Daniela D. Herrera-Balandrano, Tang-Min Chen, Xiao-Feng Lu, Xu-Chu Duan, Mahdi Shahriar, Xin-Chi Shi, Pedro Laborda, Su-Yan Wang
Summary: This study demonstrates the role of ACC deaminase in germination arrest and reveals a new strategy for grass and weed control.
Article
Materials Science, Multidisciplinary
Huilong Luo, Feng Wu, Xinyue Wang, Sisi Lin, Mengmeng Zhang, Zhenping Cao, Jinyao Liu
Summary: Wrapping bacterial cells with an adhesive drug-loadable nanocoating allows for the encoding of bacterial colonization and therapeutic modality. Encoded bacteria can colonize a wide range of biointerfaces and carry various cargoes for multimodal therapy. In vivo studies demonstrate that orally ingested encoded bacteria exhibit significantly improved intestinal colonization and synergistically enhanced treatment efficacy. This work reveals a versatile platform for advanced microbial therapy through the encoding of bacterial colonization and modality with a single-cell coating.
Article
Cell Biology
Tatiana C. Coverdell, Ruei-Jen Abraham-Fan, Chen Wu, Stephen B. G. Abbott, John N. Campbell
Summary: By analyzing gene expression and using single-cell RNA sequencing technology, this study identified molecular subtypes of nucleus ambiguus neurons and revealed their role in controlling esophageal muscle function. The results suggest that activating specific neurons may lead to esophageal muscle contraction, while activating other neurons may significantly suppress heart rate.
Review
Agriculture, Multidisciplinary
Ji-Qin Xie, Xiang Zhou, Zi-Chang Jia, Chang-Feng Su, Youjun Zhang, Alisdair R. Fernie, Jianhua Zhang, Zhi-Yan Du, Mo-Xian Chen
Summary: Disease poses a significant challenge to sustainable agricultural development. Understanding the mechanisms of host-bacteria interactions, particularly in relation to alternative splicing, is crucial for managing bacterial diseases in agriculture. This review summarizes the changes observed in alternative splicing during host-bacteria interactions and offers guidelines for plant disease management.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Medicine, Research & Experimental
Younglang Lee, Alex W. Wessel, Jiazhi Xu, Julia G. Reinke, Eries Lee, Somin M. Kim, Amy P. Hsu, Jevgenia Zilberman-Rudenko, Sha Cao, Clinton Enos, Stephen R. Brooks, Zuoming Deng, Bin Lin, Adriana A. de Jesus, Daniel N. Hupalo, Daniela G. P. Piotto, Maria T. Terreri, Victoria R. Dimitriades, Clifton L. Dalgard, Steven M. Holland, Raphaela Goldbach-Mansky, Richard M. Siegel, Eric P. Hanson
Summary: This study characterized a pediatric autoinflammatory syndrome called NEMO deleted exon 5 autoinflammatory syndrome (NDAS) in three unrelated male patients. The syndrome is caused by distinct X-linked IKBKG germline mutations that lead to overexpression of a NEMO protein isoform lacking the domain encoded by exon 5 (NEMO-Aex5). The patients exhibited increased NF-KB activation and IFN production in immune cells and blood cells.
JOURNAL OF CLINICAL INVESTIGATION
(2022)
Editorial Material
Plant Sciences
Stanislav Kopriva, Andreas P. M. Weber
Summary: In order to guarantee food security for future generations, new approaches to enhance crop productivity are needed as a result of global climate change and the growing human population causing resource scarcity and productivity declines.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Acoustics
Lihua Fan, Aliyu Idris Muhammad, Balarabe Bilyaminu Ismail, Donghong Liu
Summary: Sonodynamic antimicrobial chemotherapy (SACT) combines low-intensity ultrasound with chemotherapeutic agents to effectively combat microbial burden. With its superior penetration ability and high target specificity, SACT has emerged as a promising alternative for microbial inactivation. This treatment method has attracted increasing attention in recent years.
ULTRASONICS SONOCHEMISTRY
(2021)
Review
Microbiology
Leon M. T. Dicks, Wian Vermeulen
Summary: Cancer is a major cause of death and illness globally, with various types of cancer showing an increasing trend worldwide. Treatment methods for cancer vary, but commonly include surgery, radiotherapy, and chemotherapy. Recent research has focused on the role of bacteria and their metabolites in cancer treatment.
Article
Engineering, Electrical & Electronic
Jiangping Zhu, Changhui Zhu, Pei Zhou, Zhoumiao He, Di You
Summary: This article proposes a fringe binary encoding strategy based on genetic algorithm to reduce the phase error recovered by the temporal phase unwrapping method. An optimization equation is designed to calculate the encoding error by combining phase error and intensity error, ensuring that the optimized diffusion kernel is robust to defocusing changes. Both simulation and experiments have proved the effectiveness and accurateness of the proposed method.
IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT
(2022)
Article
Multidisciplinary Sciences
Yanyu Xiao, Jingjing Wang, Jiaqi Li, Peijing Zhang, Jingyu Li, Yincong Zhou, Qing Zhou, Ming Chen, Xin Sheng, Zhihong Liu, Xiaoping Han, Guoji Guo
Summary: Understanding the mechanism of genetic associations with human phenotypes is complicated by cellular heterogeneity and linkage disequilibrium. The authors propose an analytical framework, Huatuo, to decode the genetic variation of gene regulation at both cell-type and single-nucleotide levels.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Bin Li, Zheng Wang, Qian Chen, Kuokuo Li, Xiaomeng Wang, Yijing Wang, Qian Zeng, Ying Han, Bin Lu, Yuwen Zhao, Rui Zhang, Li Jiang, Hongxu Pan, Tengfei Luo, Yi Zhang, Zhenghuan Fang, Xuewen Xiao, Xun Zhou, Rui Wang, Lu Zhou, Yige Wang, Zhenhua Yuan, Lu Xia, Jifeng Guo, Beisha Tang, Kun Xia, Guihu Zhao, Jinchen Li
Summary: To address the challenge of accessing detailed clinical phenotypic features of patients with genetic variants, researchers developed an online database called GPCards, which integrates genetic and clinical data to provide interpretation of genotype-phenotype correlations and prioritization of candidate functional variants. This tool accelerates the interpretation of genotype-phenotype correlations in human genetic diseases and aids researchers in making faster diagnostic and treatment decisions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Gastroenterology & Hepatology
Sally Mortlock, Anton Lord, Grant Montgomery, Martha Zakrzewski, Lisa A. Simms, Krupa Krishnaprasad, Katherine Hanigan, James D. Doecke, Alissa Walsh, Ian C. Lawrance, Peter A. Bampton, Jane M. Andrews, Gillian Mahy, Susan J. Connor, Miles P. Sparrow, Sally Bell, Timothy H. Florin, Jakob Begun, Richard B. Gearry, Graham L. Radford-Smith
Summary: This study identified genetic loci associated with medically refractory ulcerative colitis (UC) through a genome wide association analysis. The findings suggest different genetic risk factors for medically refractory UC compared to non-medically refractory UC. Further research may uncover additional loci related to disease severity.
JOURNAL OF CROHNS & COLITIS
(2023)
Review
Biochemistry & Molecular Biology
Benoit J. Pons, Stineke van Houte, Edze R. Westra, Anne Chevallereau
Summary: CRISPR-Cas is a defense system in prokaryotes that protects against invasion by mobile genetic elements, such as bacteriophages. Bacteriophages can overcome CRISPR-Cas defenses by encoding anti-CRISPR proteins, which inhibit the CRISPR-Cas machinery and promote phage replication. This review summarizes the current understanding of the distribution of anti-CRISPR genes in mobile genetic elements, the ecology of phages encoding anti-CRISPR proteins, and their coevolution with bacterial defense mechanisms. The need to use more diverse and complex experimental models to better understand the impact of anti-CRISPR in mobile genetic element-host interactions is highlighted.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Computer Science, Information Systems
Hongjun Xu, Narushan Pillay
Summary: This paper proposes an alternative encoding method for the Golden code with simplified and low complexity implementation. An equivalent received signal model is constructed to derive the lower bound of average bit error probability. Additionally, a low complexity detection scheme is proposed to reduce detection complexity at high signal-to-noise ratios.
Review
Microbiology
Maura Santos Reis de Andrade da Silva, Bianca de Melo Silveira dos Santos, Camilla Santos Reis de Andrade da Silva, Carolina Santos Reis de Andrade da Silva, Luiz Fernando de Sousa Antunes, Roberta Mendes dos Santos, Carlos Henrique Barbosa Santos, Everlon Cid Rigobelo
Summary: This review discusses the combined application of PGPB and HSs to different crops and their effects on promoting plant growth and responding to abiotic stresses. The lack of research on the role of PGPB + HSs in biocontrol is also addressed, highlighting the potential for developing efficient biostimulants for sustainable agricultural management.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Yong Woong Jun, Eddy Albarran, David L. Wilson, Jun Ding, Eric T. Kool
Summary: Mitochondrial function declines with aging and neurodegeneration, largely due to accumulated mutations in mtDNA from deficient DNA repair. A fluorescent probe, UBER, was used to visualize mitochondrial BER activity, showing increased repair under oxidative stress and time delay between stress onset and BER initiation. Cells lacking MTH1 exhibited elevated demand for BER activity during extended stress, while absence of OGG1 limited glycosylation capacity.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Biswarup Jash, Eric T. Kool
Summary: In this study, we investigated the acylation reactivity of RNA 2'-OH groups and identified the strong influence of steric and inductive effects on the reaction. These findings provide insights into new strategies for enhancing conjugation and mapping of RNA.
CHEMICAL COMMUNICATIONS
(2022)
Article
Microbiology
Mericien Venzon, Ritika Das, Daniel J. Luciano, Julia Burnett, Hyun Shin Park, Joseph Cooper Devlin, Eric T. Kool, Joel G. Belasco, E. Jane Albert Hubbard, Ken Cadwell
Summary: Microbial byproducts play a crucial role in the reproductive development of nematodes by affecting their fertility and hatching abilities through alterations in arginine and aldehyde levels.
CELL HOST & MICROBE
(2022)
Article
Biochemistry & Molecular Biology
Yujeong Lee, Yoshiyuki Onishi, Lisa McPherson, Anna M. Kietrys, Marian Hebenbrock, Yong Woong Jun, Ishani Das, Shanthi Adimoolam, Debin Ji, Michael G. Mohsen, James M. Ford, Eric T. Kool
Summary: Impaired DNA repair activity is associated with increased cancer rates. This study found that certain tyrosine kinase inhibitors, such as nilotinib, can activate the repair enzyme MTH1, which cleanses oxidatively damaged nucleotides. Structural optimization resulted in compounds that strongly activate MTH1 and decrease mutagenic nucleotides in cellular DNA. These findings suggest that MTH1 activators may be a promising strategy to suppress tumorigenesis in individuals with elevated cancer risks.
ACS CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yong Woong Jun, Emily M. Harcourt, Lu Xiao, David L. Wilson, Eric T. Kool
Summary: This article presents a convenient and versatile method for general fluorescence labeling of DNAs. It utilizes deaminated DNA bases and aminooxy-substituted rotor dyes to mark label positions and trap AP sites, resulting in high emission intensities for fluorescence labeling of oligonucleotides and dsDNA.
NATURE COMMUNICATIONS
(2022)
Review
Chemistry, Multidisciplinary
Yong Woong Jun, Eric T. Kool
Summary: DNA repair enzymes play a significant role in protecting cellular DNA from damage and are closely associated with cancer and inflammation pathways. The development of new tools and methods has greatly contributed to the study of these enzymes and their potential applications in diagnostics and therapies. This article provides an overview of the development of chemical tools for studying DNA repair processes and discusses the insights gained from their application. The article also highlights the importance of future research in the field of biomedicine and human health.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Beatriz Mateo-Victoriano, Ling Zhang, Govindi Samaranayake, Cassie Due, Clara Troccoli, Julia Zaias, Nagaraj Nagathihalli, Michael Mohsen, Eric Kool, Priyamvada Rai
FREE RADICAL BIOLOGY AND MEDICINE
(2022)
Article
Chemistry, Multidisciplinary
Lu Xiao, Linglan Fang, Sayantan Chatterjee, Eric T. Kool
Summary: RNA 2'-OH acylation is widely used for structure mapping and conjugation, and depends on selective reactions with unpaired nucleotides. We prepared a range of structurally diverse acylimidazole reagents and used deep sequencing to study their reactivity and selectivity in a variety of RNA structures. Our results demonstrate that the reagent scaffold significantly affects reactivity profiles and highlight new acylating agents with altered selectivity, including compounds that show elevated selectivity within loops and reduced off-target reactivity in loop closing base pairs. We also discovered a simple reagent that is cell permeable and can map RNA structure in the presence of protein contacts, and describe reagents with elevated selectivity within small loops for site-selective labeling.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Sayantan Chatterjee, Ryuta Shioi, Eric T. Kool
Summary: The nucleophilic reactivity of RNA 2'-OH groups has been applied in various RNA-related processes. In this study, it is discovered that activated small-molecule sulfonyl species can retain their reactivity in water. Reactions with ribose 2'-OH show high yields, especially for aryl sulfonyltriazole species. Additionally, an azide-substituted sulfonyltriazole reagent is developed for labeling RNA via click chemistry.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Yong Woong Jun, Melis Kant, Erdem Coskun, Takamitsu A. A. Kato, Pawel Jaruga, Elizabeth Palafox, Miral Dizdaroglu, Eric T. T. Kool
Summary: High-temperature cooking damages DNA in food, which can then enter the cellular DNA and lead to genetic risks.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Linglan Fang, Lu Xiao, Yong Woong Jun, Yoshiyuki Onishi, Eric T. T. Kool
Summary: The presence of a hydroxyl group at the 2'-position in ribose makes RNA susceptible to hydrolysis. In this study, reversible 2'-OH acylation was presented as a general strategy to preserve RNA stability. High-yield polyacylation of 2'-hydroxyls effectively protected RNAs from degradation, and subsequent treatment with nucleophilic reagents removed acylation adducts and recovered a wide range of RNA functions.
Article
Chemistry, Multidisciplinary
Ryuta Shioi, Lu Xiao, Sayantan Chatterjee, Eric T. Kool
Summary: The reactivity of RNA 2'-OH groups with acylating agents has been studied for high-yield conjugation of RNA strands. This study focuses on the stereoselectivity of chiral acylimidazoles in RNA reactions. The results reveal that positional selectivity and reactivity vary greatly with local RNA macro-chirality, and the chirality of the reagents has a significant impact on their reactivity. This study demonstrates new chemical strategies for selective RNA modification and probing.
Article
Biochemical Research Methods
Reema Baskar, Amy F. Chen, Patricia Favaro, Warren Reynolds, Fabian Mueller, Luciene Borges, Sizun Jiang, Hyun Shin Park, Eric T. Kool, William J. Greenleaf, Sean C. Bendall
Summary: Master transcription factors regulate cell states by driving gene-expression programs, and their abundance affects cell fate at the chromatin level. InTAC-seq method allows the study of the relationship between protein abundance and gene regulation in cells.
CELL REPORTS METHODS
(2022)
Article
Biochemistry & Molecular Biology
Lu Xiao, Linglan Fang, Eric T. Kool
Summary: The reactivity of RNA 2'-OH acylation has been extensively studied in this research. The results show that there is a wide range of reactivity among single-stranded RNA sequences, with nearest neighbors playing a significant role. Interestingly, certain small loops exhibit much higher reactivity compared to single-stranded RNAs, which is attributed to conformational constraints.
CELL CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Sergio M. Marques, Michaela Slanska, Klaudia Chmelova, Radka Chaloupkova, Martin Marek, Spencer Clark, Jiri Damborsky, Eric T. Kool, David Bodnar, Zbynek Prokop
Summary: HaloTag labeling technology has revolutionized protein chemistry and cellular biology, and a systematic analysis of different ligands has led to the discovery of an optimal protein tag selection protocol, eliminating the need for expensive and complex protein engineering.