Article
Cell Biology
Lorena Suarez-Artiles, Tilman Breiderhoff, Rossana Girardello, Hannes Gonschior, Sophie Rodius, Antoine Lesur, Ulf Reimer, Evelyn Ramberger, Daniel Perez-Hernandez, Dominik Muller, Philipp Mertins, Gunnar Dittmar
Summary: This study investigates the interaction of the C-terminal tails of the Claudin family with other proteins, revealing their potential involvement in specific biological processes in epithelial cells and their regulation by post-translational modifications.
Article
Microbiology
Shan Zhang, Weizhi Song, Louis-Felix Nothias, Sneha P. Couvillion, Nicole Webster, Torsten Thomas
Summary: This study demonstrates the compartmentalization of different chemical functionalities between sponge hosts and their microbial symbionts, and provides new insights into the function of sponge holobionts.
Article
Chemistry, Physical
Meryem Eren, Nurcan Tuncbag, Hyunbum Jang, Ruth Nussinov, Attila Gursoy, Ozlem Keskin
Summary: The study reveals that KRas4B exhibits partner-specific dynamics when interacting with different proteins, shedding light on the intricate protein-protein interactions involved in cellular signaling.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biotechnology & Applied Microbiology
Xudong Liu, Zhinan Wu, Tongyuan Hu, Xiaoqian Lin, Hewei Liang, Wenxi Li, Xin Jin, Liang Xiao, Xiaodong Fang, Yuanqiang Zou
Summary: This study provides new insights into the genomic diversity analysis of L. acidophilus and uncovers the ecological adaptation of specific strains.
JOURNAL OF APPLIED MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Stefan Reber, Daniel Jutzi, Helen Lindsay, Anny Devoy, Jonas Mechtersheimer, Brunno Rocha Levone, Michal Domanski, Eva Bentmann, Dorothee Dormann, Oliver Muehlemann, Silvia M. L. Barabino, Marc-David Ruepp
Summary: Liquid-liquid phase separation (LLPS) of proteins and RNAs is critical in the formation of membrane-less organelles, leading to biomolecular condensates with diverse biological functions and disease implications. The Fused in Sarcoma (FUS) protein undergoes LLPS and its mutations are linked to Amyotrophic Lateral Sclerosis (ALS-FUS). The study shows that LLPS shapes the interactome of FUS in cells, affecting its function and disease outcomes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Chengcai Zhang, Huadong Ren, Xiaohua Yao, Kailiang Wang, Jun Chang
Summary: This study investigated the molecular mechanisms underlying flavonoid biosynthesis in pecan nuts and identified key genes and transcription factors that showed high correlation with flavonoid content. These findings are important for understanding the biosynthesis of flavonoids and accelerating the breeding of high-quality pecan varieties.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Environmental Sciences
Chaogang Wang, Mingyang Du, Zhuxiang Jiang, Rihao Cong, Wei Wang, Guofan Zhang, Li Li Acdefg
Summary: This study investigates the role of protein phosphorylation modifications in the molecular regulation network under heat stress in oysters, revealing the molecular mechanisms underlying the differential thermal responses between two oyster species at the phosphorylation level.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Agronomy
Shengyu Li, Jiali Zeng, Zhao Zheng, Qi Zhou, Shaona Chen, Yixiong Zheng, Xiaorong Wan, Bin Yang
Summary: A comparative transcriptome analysis of two peanut accessions revealed differences in DEGs related to cell wall remodeling, hormone signaling, transcriptional regulation, and oxidative stress, providing insights into the differences in seed vigor between varieties.
Article
Biochemistry & Molecular Biology
Liping Zhu, Yao Su, Zhiheng Ma, Lizhong Guo, Song Yang, Hao Yu
Summary: This study used label-free comparative proteomic analysis to investigate the protein expression profile of Hypsizygus marmoreus mycelia under different light qualities and darkness. Differential expression proteins were identified and analyzed, revealing the involvement of light stress in primary metabolism, glycolysis/gluconeogenesis, MAPK, proteasome, and carbohydrate-active enzyme pathways.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Multidisciplinary Sciences
Hao Gong, Bin Han
Summary: This study investigates the genetic introgression of Asian cultivated rice using genome-wide variation data. It identifies 13 significantly high introgression loci between the tropical japonica and indica populations. The study also highlights the important role of genetic introgression in determining the phenotype and domestication process.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Paula Montana-Lozano, Manuela Moreno-Carmona, Mauricio Ochoa-Capera, Natalia S. Medina, Jeffrey L. Boore, Carlos F. Prada
Summary: This study conducts a comparative genomic analysis of 2831 vertebrate mitochondrial genomes and reveals errors in gene annotation, particularly in tRNAs. It also finds significant variations in gene rearrangement proportions among different taxonomic classes, with distinct rearrangement patterns and hotspots within each class.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Yeonji Chang, Gyubum Lim, Won-Ki Huh
Summary: Research has shown that TORC1 has functional relationships with mRNA, interacts with mRNP complexes, and inhibits the activity of translational repressor protein Scd6 through phosphorylation.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Immunology
Hai-Chao Song, Bin-Tong Yang, Tong Zhao, Yu-Feng Sun, Jin-Hua Zhou, Xiao-Feng Shan, Ai-Dong Qian, Wen-Chao Sun, Yuan-Huan Kang
Summary: This study analyzed 39 strains of A. veronii using comparative genomics, identifying 1993 core genes that are essential for maintaining the basic characteristics of A. veronii. The AMC34 strain may not belong to A. veronii, and the genetic relationship among the other 38 strains is relatively close.
MICROBIAL PATHOGENESIS
(2021)
Article
Biology
Dawn M. Wenzel, Douglas R. Mackay, Jack J. Skalicky, Elliott L. Paine, Matthew S. Miller, Katharine S. Ullman, Wesley Sundquist, Aurelien Roux
Summary: In this study, the interactions between human MIT domains and ESCRT-III tails were comprehensively mapped and quantified. Several new interactions were discovered, and the structure of the SPASTIN MIT domain in complex with the IST1 C-terminal tail was reported. The study also revealed the localization and functions of three MIT enzymes in cytokinetic abscission.
Article
Medicine, Research & Experimental
Aneesha Dasgupta, Paige C. Arneson-Wissink, Rebecca E. Schmitt, Dong Seong Cho, Alexandra M. Ducharme, Tara L. Hogenson, Eugene W. Krueger, William R. Bamlet, Lizhi Zhang, Gina L. Razidlo, Martin E. Fernandez-Zapico, Jason D. Doles
Summary: Approximately 80% of pancreatic cancer patients suffer from cachexia, and one-third die due to cachexia-related complications. However, there are currently no FDA-approved therapies for cachexia. In this study, a aged model of pancreatic cancer cachexia was generated and compared with young tumor-bearing mice. The antiwasting compound, 3-methyladenine (3-MA), was identified and shown to have potential antitumor effects. In addition, the gene Perp was implicated as a target of 3-MA, and its reduction inhibited tumor cell growth.
Article
Optics
Ran Huang, S. K. Ozdemir, Jie-Qiao Liao, Fabrizio Minganti, Le-Man Kuang, Franco Nori, Hui Jing
Summary: This study demonstrates the emergence of single-photon blockade in a Kerr microring resonator due to EP-induced asymmetric coupling and nonlinearity-induced anharmonic energy-level spacing. By tuning the EP position, quantum correlations can be controlled, opening up opportunities for the fabrication and utilization of single-photon quantum EP devices.
LASER & PHOTONICS REVIEWS
(2022)
Article
Multidisciplinary Sciences
Huiting Jing, Yang Liu, Jinghua Zhao
Summary: In the field of financial risk measurement, the assumption of normalcy is often broken, and the Asymmetric Laplace distribution provides a better option for modeling financial data. This distribution reveals the properties of empirical financial data sets better than the normal model. Therefore, it is a simple, creative, and useful choice for calculating risk measures.
Article
Integrative & Complementary Medicine
Yingying Cheng, Guofu Li, Hui Jing, Shasha Yuan, Lei Zhang, Wen Cheng
Summary: This study evaluated the effectiveness of quantitative shear wave elastography (SWE) to predict axillary lymph node metastasis in invasive breast cancer. The elasticity index (EI) of SWE was found to be closely associated with pathologic results. Joint use of SWE and B-mode ultrasound (BUS) showed great potential in predicting metastatic lymph nodes.
EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE
(2022)
Article
Construction & Building Technology
Zetao Zhao, Xiongyan Li, Renjie Liu, Suduo Xue, Tifeng Liu, Qinxin Fan, Hui Jing, Majid Dezhkam
Summary: This study investigates the influence of substructures on the seismic performance of the suspen-dome structure. By replacing the complex concrete substructures with steel substructures in shaking table tests, the accurate and effective method is proposed. The results demonstrate that substructures have a significant impact on the seismic performance of the suspen-dome, highlighting the importance of considering them in the analysis and design stages.
PROCEEDINGS OF THE INSTITUTION OF CIVIL ENGINEERS-STRUCTURES AND BUILDINGS
(2022)
Letter
Chemistry, Physical
Dan Su, Tatsiana Kosciuk, Hening Lin
Summary: This article concludes that binding affinity is crucial for in vivo substrate specificity and proposes a method to identify substrate proteins for enzymes by utilizing existing interactome data. The Reply aims to clarify important points in the original article.
Article
Biology
Lei Yuan, Peiyao Li, Huiru Jing, Qian Zheng, Hui Xiao
Summary: This study reveals a unique mechanism for maintaining appropriate levels of the phagocytic receptor CED-1, which is responsible for apoptotic cell clearance. The E3 ubiquitin ligase TRIM-21, along with other proteins, catalyzes the poly-ubiquitination of CED-1, leading to its degradation and maintaining its proper levels for effective cell corpse clearance.
Article
Biochemistry & Molecular Biology
Ananya Anmangandla, Yuxiang Ren, Qin Fu, Sheng Zhang, Hening Lin
Summary: Protein post-translational modifications play a vital role in regulating cellular functions. KAT2A, an important acetyltransferase, has been shown to have activity with various substrates, but acetylation remains its most efficient activity.
Article
Multidisciplinary Sciences
Arash Latifkar, Fangyu Wang, James J. Mullmann, Elena Panizza, Irma R. Fernandez, Lu Ling, Andrew D. Miller, Claudia Fischbach, Robert S. Weiss, Hening Lin, Richard A. Cerione, Marc A. Antonyak
Summary: This study reveals a previously unknown role for IGF2BP2 in mediating the degradation of a messenger RNA transcript essential for lysosomal function, which has significant biological and disease consequences.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Garrison Komaniecki, Maria Del Carmen Camarena, Eric Gelsleichter, Rachel Mendoza, Mark Subler, Jolene J. Windle, Mikhail G. Dozmorov, Zhao Lai, Devanand Sarkar, Hening Lin
Summary: Nonalcoholic fatty liver disease is a major risk factor for hepatocellular carcinoma and involves lipid accumulation, inflammation, and tumorigenesis. This study discovered that AEG-1 is palmitoylated at residue cysteine 75 (Cys75) and that mutation of Cys75 to serine (Ser) abolishes this palmitoylation. Further experiments in mice revealed that the Cys75 mutation activates signaling pathways related to cell proliferation, motility, inflammation, angiogenesis, and lipid accumulation in hepatocytes. This finding suggests that palmitoylation restricts the oncogenic and NASH-promoting functions of AEG-1.
Review
Biochemistry & Molecular Biology
Hening Lin
Summary: Small-molecule inhibitors of enzymes are widely used in reverse chemical genetics to explore biology and therapeutic opportunities. However, they may not produce the same phenotype as genetic perturbations due to substrate-selective or substrate-dependent effects. This review discusses examples of substrate-selective inhibitors and emphasizes their advantages over biologics, presenting exciting opportunities for chemical biologists and medicinal chemists.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Hening Lin
Summary: Dr. Christopher T. Walsh, a giant in enzymology, passed away in January 2023. This summary briefly highlights his numerous accomplishments in research, academic administration, scientific and industry advising, as well as teaching and mentoring of students and postdoctoral fellows. He has left behind a rich legacy that will continue to inspire generations of scientists.
ACS CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Thanh Tu Ho, Changmin Peng, Edward Seto, Hening Lin
Summary: This article reports the development of trapoxin A analogues as potent and selective inhibitors of HDAC11, an enzyme involved in removing long-chain fatty acyl groups from proteins. One of the analogues, TD034, exhibits nanomolar potency in enzymatic assays and inhibits the defatty acylation of a known HDAC11 substrate in cells. The high potency and selectivity of TD034 could lead to the development of HDAC11 inhibitors for various biological and therapeutic applications.
ACS CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ananya Anmangandla, Sadhan Jana, Kewen Peng, Shamar D. Wallace, Saket R. Bagde, Bryon S. Drown, Jiashu Xu, Paul J. Hergenrother, J. Christopher Fromme, Hening Lin
Summary: Researchers have developed a robust fluorescence polarization assay for various viral and human macrodomains, including SARS-CoV-2 Macro1, using a novel tracer TAMRA-ADPr. The assay identified GS441524 as a highly selective inhibitor of SARS-CoV-2 Macro1 over other macrodomains.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Zhipeng A. Wang, Jonathan W. Markert, Samuel D. Whedon, Maheeshi Yapa Abeywardana, Kwangwoon Lee, Hanjie Jiang, Carolay Suarez, Hening Lin, Lucas Farnung, Philip A. Cole
Summary: The reversible acetylation of histone lysine residues is controlled by the action of acetyltransferases and deacetylases (HDACs), which regulate chromatin structure and gene expression. One member of the HDAC family, Sirt6, efficiently deacetylates several histone H3 acetylation sites on nucleosomes. The structure of Sirt6 bound to a nucleosome reveals its extensive interactions with H2A/H2B acidic patch and nucleosomal DNA, providing insights into how HDACs target and regulate chromatin.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Michael R. Smith, Le Zhang, Yizhen Jin, Min Yang, Anusha Bade, Kevin D. Gillis, Sadhan Jana, Ramesh Naidu Bypaneni, Timothy E. Glass, Hening Lin
Summary: Maintaining the balance of amino acids is important for cell survival and dysfunction of nutrient balance can lead to diseases such as diabetes. In this study, a novel fluorescent sensor called NS560 was developed to detect 18 proteogenic amino acids in mammalian cells. By using NS560, amino acid pools were identified in lysosomes, late endosomes, and near the rough endoplasmic reticulum. Furthermore, the study revealed that Cathepsin L (CTSL) is the target of chloroquine, leading to the accumulation of amino acids in large cellular foci.
ACS CENTRAL SCIENCE
(2023)
