Article
Plant Sciences
Huihui Fang, Zhenyuan Yu, Kehong Xing, Lingyi Zhou, Yuke Shao, Xiaofang Zhang, Yanxi Pei, Lu Zhang
Summary: Numerous studies have shown that hydrogen sulfide (H2S) functions as a gasotransmitter in various biological processes. However, its involvement in sulfur metabolism and/or Cys synthesis makes its role as a signaling molecule unclear. In this study, we found that exogenous H2S fumigation and Cys treatment affected the production rate and content of endogenous H2S and Cys. Transcriptomic analysis revealed that H2S regulates gene expression independently of Cys, mainly involved in plant hormone signal transduction and plant-pathogen interaction.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Medicine, Research & Experimental
Zhengrui Li, Rao Fu, Xufeng Huang, Xutao Wen, Ling Zhang
Summary: This study aimed to assess the correlation between oral microbiota and the extent of bone resorption in ORN patients. The results showed that the ORN group had higher microbial abundance and species diversity, and specific microbial communities were potentially associated with ORN. In addition, an imbalance in the oral microbiota may disrupt bone regeneration by regulating specific metabolic pathways that increase osteoclastic activity. Therefore, radiation-induced ORN is associated with significant changes in the oral microbiota.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Cardiac & Cardiovascular Systems
Jiangming Sun, Pratibha Singh, Annelie Shami, Ewelina Kluza, Mengyu Pan, Djordje Djordjevic, Natasha Barascuk Michaelsen, Cecilia Kennback, Nicole N. van der Wel, Marju Orho-Melander, Jan Nilsson, Ivan Formentini, Karin Conde-Knape, Esther Lutgens, Andreas Edsfeldt, Isabel Goncalves
Summary: This study identifies the specific locations of atherosclerotic plaque ruptures in human carotid arteries and the underlying mechanisms. The proximal and most stenotic regions are found to be vulnerable to plaque rupture. RNA sequencing reveals differentially expressed genes that distinguish these regions, with matrix metallopeptidase 9 being associated with atherosclerosis risk. These findings provide insights for the development of targeted therapies against plaque rupture.
JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Yankai Jiang, Xinyue Cao, Haibin Wang
Summary: By identifying specific mutations that lead to limblessness in a pig, this research sheds light on the evolutionary trajectory of limb development in vertebrates. These findings have implications for further exploration in human genetics and evolutionary biology.
Article
Agronomy
Ziqian Cui, Shaodong Liu, Changwei Ge, Qian Shen, Siping Zhang, Huijuan Ma, Ruihua Liu, Xinhua Zhao, Ruida Liu, Pengzhen Li, Hongchen Wang, Qidi Wu, Chaoyou Pang, Jing Chen
Summary: Two significantly associated regions were identified for root diameter traits on chromosome A05 and D04, respectively. Two candidate genes related to root development were also identified. Silencing these genes resulted in reduced root length and surface area. This study provides important insights for the cultivation and improvement of cotton varieties.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Endocrinology & Metabolism
Neelam Hassan, Celia L. L. Gregson, Haotian Tang, Marc van der Kamp, Paul Leo, Aideen M. McInerney-Leo, Jie Zheng, Maria Luisa Brandi, Jonathan C. Y. Tang, William Fraser, Michael D. Stone, Elin Grundberg, Matthew A. Brown, Emma L. Duncan, Jonathan H. Tobias
Summary: Rare heterozygous loss-of-function variants in the GALNT3 gene may cause osteoporosis without altering phosphate concentration. These findings suggest that GALNT3 may affect bone mineral density through pathways other than FGF23 regulation, providing potential novel drug targets for osteoporosis.
JOURNAL OF BONE AND MINERAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Rayan Fakih, Veronique Sauve, Kalle Gehring
Summary: Parkin and PINK1 regulate a mitochondrial quality control system that is mutated in some early onset forms of Parkinson's disease. Recently, an alternative feed-forward mechanism was identified that bypasses the need for parkin phosphorylation. This study reveals the structure of parkin activated through this feed-forward mechanism and provides insights into the differences in specificity and affinity of the binding sites.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Oncology
Lanlan Wang, Yali Ma, Wenjie Han, Qiumin Yang, Muhammad Jamil
Summary: By performing Whole Exome Sequencing (WES) on Pakistani lung cancer patients, this study identified clinically important pathogenic mutations in 6 DNA repair genes and revealed their potential implications on prognosis. Down-regulation of these mutated genes and hypermethylation in their promoters were observed, indicating a potential convergence of genetic and epigenetic factors driving genomic instability in lung cancer cells. These findings contribute to our understanding of lung cancer susceptibility and offer potential avenues for targeted therapeutic interventions in Pakistani patients.
AMERICAN JOURNAL OF CANCER RESEARCH
(2023)
Article
Cell Biology
Xinyu Yang, Di Lu, Rui Wang, Zhengxing Lian, Zuyuan Lin, Jianyong Zhuo, Hao Chen, Modan Yang, Winyen Tan, Mengfan Yang, Xuyong Wei, Qiang Wei, Shusen Zheng, Xiao Xu
Summary: Our study identified 11 different cell types in transplanted livers, with a highly complex ecosystem primarily shaped by myeloid-derived cell subsets that transition between different states and interact mutually. In transplanted steatotic livers, a pro-inflammatory phenotype of Kupffer cells (KCs) with high expression of colony-stimulating factor 3 (CSF3) was found to potentially contribute to fatty graft injury. Additionally, a subset of dendritic cells (DCs) with highly expressing XCR1 was correlated with CD8(+) T cells, mediating severer steatotic liver damage by I/R injury.
CELL PROLIFERATION
(2021)
Article
Cell Biology
Archita Agrawal, Pu Ni, Rafiou Agoro, Kenneth E. White, Richard D. DiMarchi
Summary: FGF23 interacts with a FGFR/KL-receptor complex and has two independent KL-interaction sites at its C terminus, the loss of either leading to protein inactivation. The identification of the second KL-association site provides a potential for enhanced biological effects.
Article
Biochemical Research Methods
Christoffer Norn, Ingemar Andre
Summary: Thermodynamic stability plays a crucial role in protein evolution, affecting mutation rates and residue-residue covariation. By simulating protein evolution and calculating protein stability, researchers have found that stability is related to mutation rates and the spectrum of accepted mutations. These findings provide mechanistic insights into the evolutionary consequences of protein stability variation.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Matthew McCallum, Anna De Marco, Florian Lempp, M. Alejandra Tortorici, Dora Pinto, Alexandra C. Walls, Martina Beltramello, Alex Chen, Zhuoming Liu, Fabrizia Zatta, Samantha Zepeda, Julia di Iulio, John E. Bowen, Martin Montiel-Ruiz, Jiayi Zhou, Laura E. Rosen, Siro Bianchi, Barbara Guarino, Chiara Silacci Fregni, Rana Abdelnabi, Shi-Yan Caroline Foo, Paul W. Rothlauf, Louis-Marie Bloyet, Fabio Benigni, Elisabetta Cameroni, Johan Neyts, Agostino Riva, Gyorgy Snell, Amalio Telenti, Sean P. J. Whelan, Herbert W. Virgin, Davide Corti, Matteo Samuele Pizzuto, David Veesler
Summary: The study identifies 41 human monoclonal antibodies that recognize the N-terminal domain of the SARS-CoV-2 spike protein and exhibit strong neutralizing activity. These antibodies inhibit cell-to-cell fusion, activate effector functions, and protect animals from virus challenge, highlighting the importance of NTD-specific neutralizing antibodies for protective immunity and vaccine development. Several SARS-CoV-2 variants with mutations in the NTD supersite suggest ongoing selective pressure on the virus.
Article
Biochemistry & Molecular Biology
Martina Rosato, Sven Stringer, Titia Gebuis, Iryna Paliukhovich, Ka Wan Li, Danielle Posthuma, Patrick F. Sullivan, August B. Smit, Ronald E. van Kesteren
Summary: A combined cellomics and proteomics approach was used to disentangle polygenic risk in schizophrenia by searching for shared neuronal morphology and cellular pathway phenotypes of candidate schizophrenia risk genes. It was found that certain schizophrenia risk genes shared a neuronal phenotype marked by a reduction in synapse numbers and converged onto the syntaxin-mediated neurotransmitter release pathway. This study provides new biological functions for schizophrenia risk genes and supports the idea that polygenic risk results from multiple small impacts on common neuronal signaling pathways.
MOLECULAR PSYCHIATRY
(2021)
Article
Allergy
Hui Li, Huaqi Wang, Leon Sokulsky, Shaoxia Liu, Rui Yang, Xiaojie Liu, Lujia Zhou, Juan Li, Chun Huang, Fangfang Li, Xu Lei, Hongxia Jia, Jiuling Cheng, Fuguang Li, Ming Yang, Guojun Zhang
Summary: This study identified significantly elevated levels of monocytes, CD8(+) T cells, and macrophages in the bronchoalveolar lavage fluid of patients with asthma exacerbation. Additionally, a complicated molecular framework involving a set of cytokines and intracellular transduction regulators shared across multiple cell clusters was discovered. Moreover, core exacerbation-associated modules activated included pathways such as eukaryotic initiation factor 2 signaling and C-X-C chemokine receptor type 4 signaling in specific cell populations associated with infection.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Xiaojie Zhang, Soo Jung Lee, Michael M. Wang
Summary: In CADASIL patients, NOTCH3 protein is cleaved at a high level at Asp121, while control vessels harbor only a small amount of cleaved NOTCH3. Similar to other neurodegenerative conditions, chronic brain vascular disease features proteolysis of pathological proteins at multiple sites, which may generate small pathological peptides.
SCIENTIFIC REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Ryan J. Emenecker, Lucia C. Strader
Article
Plant Sciences
Jose A. Trujillo-Hernandez, Laetitia Bariat, Tara A. Enders, Lucia C. Strader, Jean-Philippe Reichheld, Christophe Belin
JOURNAL OF EXPERIMENTAL BOTANY
(2020)
Review
Biochemistry & Molecular Biology
Jeffrey R. Allen, Edward G. Wilkinson, Lucia C. Strader
Summary: Protein interactions are crucial in cell biology, where modular protein interaction domains play a central role in directing specific biological outcomes. These domains have diverse functions and contribute to the formation of complex protein interaction networks.
Article
Cell Biology
Ryan J. Emenecker, Alex S. Holehouse, Lucia C. Strader
Summary: Biomolecular condensates are non-stoichiometric assemblies that concentrate biomolecules spatially and play a key role in cellular organization. Proteins with oligomerization domains and intrinsically disordered regions can drive higher-order assembly. This study investigated the aging, material properties, and protein oligomeric state of biomolecular condensates in vivo, focusing on their morphological and material properties influenced by amino acid composition and higher- and lower-order oligomers abundance within individual condensates.
CELL COMMUNICATION AND SIGNALING
(2021)
Review
Plant Sciences
Lucia Strader, Dolf Weijers, Doris Wagner
Summary: This article reviews new findings on the function of plant transcription factors and their role in shaping transcription in the context of chromatin.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Peng Zhou, Tara A. Enders, Zachary A. Myers, Erika Magnusson, Peter A. Crisp, Jaclyn M. Noshay, Fabio Gomez-Cano, Zhikai Liang, Erich Grotewold, Kathleen Greenham, Nathan M. Springer
Summary: Changes in gene expression are crucial for responses to abiotic stress. Transcriptome profiling of heat- or cold-stressed maize genotypes reveals many alterations in transcript abundance. By analyzing expression responses in multiple genotypes and identifying cis- or trans-regulatory variation, predictive models of gene expression responses for thermal stress-responsive genes can be developed. Models focusing on unmethylated regions near the transcription start sites (TSSs) show improved accuracy, suggesting that different genes may have varying response dynamics to stress.
Editorial Material
Plant Sciences
Ronald Pierik, Christian Fankhauser, Lucia C. Strader, Neelima Sinha
Summary: Plasticity in plant architecture influences plant performance by utilizing dedicated molecular networks.
Editorial Material
Biochemistry & Molecular Biology
Katelyn Sageman-Furnas, Lucia Strader
Review
Biochemistry & Molecular Biology
Marcelo Rodrigues Alves de Figueiredo, Lucia C. Strader
Summary: This review focuses on the regulation of transcriptional events by the plant hormone auxin through controlled degradation of Aux/IAA proteins. It examines the composition and function of each structural motif of Aux/IAA and highlights recent studies on the N-terminal disordered regions, formation of secondary structure within these regions, and post-translational modifications that affect Aux/IAA function and stability. The authors propose that structural variations between Aux/IAA family members can be tuned for different levels of transcriptional repression and degradation dynamics.
TRENDS IN BIOCHEMICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Hongwei Jing, David A. Korasick, Ryan J. Emenecker, Nicholas Morffy, Edward G. Wilkinson, Samantha K. Powers, Lucia C. Strader
Summary: Auxin plays a critical role in regulating plant growth and development through the transcriptional responses mediated by ARF transcription factors. This study identifies a novel F-box protein named AFF1 that interacts with ARF19 and ARF7 to regulate their accumulation, condensation, and nucleo-cytoplasmic partitioning. Mutants defective in AFF1 display attenuated auxin responsiveness and developmental defects, revealing the importance of AFF1-mediated regulation of ARF proteins in auxin response and plant development.
NATURE COMMUNICATIONS
(2022)
Editorial Material
Biochemistry & Molecular Biology
Emilio Gutierrez-Beltran, Lucia Strader, Peter Bozhkov
Review
Biochemistry & Molecular Biology
Sterling Field, Geng-Jen Jang, Caroline Dean, Lucia C. Strader, Seung Y. Rhee
Summary: This review discusses recent studies on biomolecular condensates in plant development and examines the challenges faced in fully understanding their functional roles. While descriptive examples of biomolecular condensate formation in plant developmental biology are abundant, the mechanistic understanding has only recently emerged. The article presents recent examples of how biomolecular condensates potentially contribute to different stages of the plant life cycle, grouped based on their putative molecular functions such as sequestering interacting components, enhancing dwell time, and interacting with cytoplasmic biophysical properties in response to environmental change. The authors also highlight the challenges and opportunities for further research in deciphering the molecular mechanisms underlying the diverse roles of biomolecular condensates in plant life.
Article
Biochemistry & Molecular Biology
Hongwei Jing, Lucia C. Strader
Summary: Auxin plays a crucial role in regulating plant development, with its effects on transcription mediated by the ARF family of transcription factors. ARFs tightly control specific auxin responses that are essential for proper plant growth and development. Recent research has highlighted the importance of regulated ARF protein accumulation and ARF nucleo-cytoplasmic partitioning in determining auxin transcriptional outputs. This review explores these recent findings and discusses the potential of regulated ARF accumulation in driving auxin responses in plants.
Article
Plant Sciences
Zhikai Liang, Sarah N. Anderson, Jaclyn M. Noshay, Peter A. Crisp, Tara A. Enders, Nathan M. Springer
Summary: This study reveals that although TEs can generate transcripts under heat or cold stress conditions, genome-wide activation of TEs did not occur. There is substantial variation in the stress-responsive expression of TE families among different genotypes, with the driving factors being largely concentrated on specific elements within TE families lacking DNA methylation. The differences in TE expression between genotypes are attributed to genetic and epigenetic variations, where fully methylated elements tend to be inactive while those with regions lacking DNA methylation are more likely to be expressed.