Article
Environmental Sciences
Xin Li, He-Fei Sun, Jia-Hui Fan, Yue-Ying Li, Lian-Ju Ma, Lan-Lan Wang, Xue-Mei Li
Summary: This study examined the effects of endophyte inoculation on the growth, SPAD value, chlorophyll fluorescence, and transcriptome response of rice seedlings under Pb stress. The results showed that endophyte inoculation significantly improved various parameters, including plant height, SPAD value, and photosynthesis-related factors. RNA-seq analysis revealed differentially expressed genes involved in various processes, such as photosynthesis, oxidative detoxification, hormone synthesis, and signal transduction. These findings provide insights into the molecular mechanisms underlying the interaction between endophyte and plants under heavy metal stress.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Nutrition & Dietetics
Ruopeng Yang, Xiu Chen, Qiang Huang, Chuying Chen, Kannan R. R. Rengasamy, Jinyin Chen, Chunpeng (Craig) Wan
Summary: The study explores a novel combination antifungal therapy of cinnamaldehyde, eugenol, or carvacrol formulated into nanoemulsion to enhance the solubility and stability of essential oils. The compound nanoemulsion showed significant inhibitory effects on Penicillium digitatum in a dose-dependent manner. RNA-seq analysis revealed differentially expressed genes and enriched pathways associated with the antifungal activity.
FRONTIERS IN NUTRITION
(2021)
Article
Immunology
Daniel Stratis, Guy Trudel, Lynda Rocheleau, Martin Pelchat, Odette Laneuville
Summary: This study characterized the molecular response of the immune system in astronauts transitioning to and from long-duration spaceflight by analyzing changes in leukocyte transcriptomes. The results showed that entering space led to changes in gene expression and immune suppression, while returning to Earth resulted in immune reactivation.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Plant Sciences
Keyvan Esmaeilzadeh-Salestani, Masoud Tohidfar, Rahele Ghanbari Moheb Seraj, Banafsheh Khaleghdoust, Indrek Keres, Hashem Marawne, Evelin Loit
Summary: This study compares the effects of organic and mineral nitrogen fertilizers on gene activity in barley. The results show that mineral nitrogen fertilizer treatment leads to a higher number of differentially expressed genes compared to organic nitrogen fertilizer treatment. Pathways related to amino acid synthesis and ribosomal activities are upregulated in mineral fertilizer treatment, while pathways related to starch and sucrose metabolism and carotenoid biosynthesis are downregulated. Organic nitrogen fertilizer treatment enriches pathways related to phenylpropanoid biosynthesis and plant-pathogen interaction. These findings provide insights into the genetic regulation of barley growth in field conditions and can guide the development of sustainable cropping practices and low nitrogen input varieties.
Article
Environmental Sciences
Liqing Zang, Yasuhito Shimada, Hideto Miyake, Norihiro Nishimura
Summary: This study examined the toxicity and safety of UVC exposure in zebrafish embryos and the corresponding molecular mechanisms. The research found that 4.5 mJ/cm(2) was the limit dosage that the internal biodefense system of zebrafish embryos can protect against UVC radiation. Transcriptome analysis revealed the molecular mechanisms underlying the response of zebrafish embryos to UVC irradiation.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Article
Multidisciplinary Sciences
Oliver J. Ziff, Jacob Neeves, Jamie Mitchell, Giulia Tyzack, Carlos Martinez-Ruiz, Raphaelle Luisier, Anob M. Chakrabarti, Nicholas McGranahan, Kevin Litchfield, Simon J. Boulton, Ammar Al-Chalabi, Gavin Kelly, Jack Humphrey, Rickie Patani
Summary: Amyotrophic Lateral Sclerosis (ALS) is characterized by motor neuron degeneration, predominantly associated with TDP-43 proteinopathy. This study integrates datasets of iPSC-derived motor neurons and post-mortem tissues to identify a heightened DNA damage response and accumulation of somatic mutations in ALS. The activation of p53 signaling is robust in ALS, with stronger activation in C9orf72 repeat expansions and weaker activation in SOD1 and FUS mutations. TDP-43 depletion enhances p53 activation, linking it functionally to ALS pathogenesis.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Chiara Magri, Erika Vitali, Sara Cocco, Edoardo Giacopuzzi, Marco Rinaudo, Paolo Martini, Alessandro Barbon, Claudio Grassi, Massimo Gennarelli
Summary: This study provides a comprehensive molecular characterization of the 3xTg-AD mouse and suggests that blood gene expression may serve as new biomarkers for identifying AD progression and treatment effects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Ronghua Zhang, Haibi Li, Yiyun Gui, Jinju Wei, Kai Zhu, Hui Zhou, Prakash Lakshmanan, Lianying Mao, Manman Lu, Junxian Liu, Youxiong Que, Song Li, Xihui Liu
Summary: This study used RNA sequencing to analyze the transcriptome changes in different sensitive sugarcane cultivars treated with PBZ, and identified differentially expressed genes associated with PBZ response. The reliability of the RNA-seq data was confirmed through validation experiments, revealing the molecular mechanisms underlying resistance to PBZ in sugarcane.
Article
Medicine, Research & Experimental
Alexander Frohlich, Abigail L. Pfaff, Vivien J. Bubb, John P. Quinn, Sulev Koks
Summary: This study analyzed differential gene expression in amyotrophic lateral sclerosis (ALS) using cerebrospinal fluid (CSF) RNA-sequencing data. The affected genes were found to be enriched in several pathways associated with the disease. Additionally, the expression of previously identified potential biomarkers was significantly higher in ALS individuals, providing insight into biomarker development.
EXPERIMENTAL BIOLOGY AND MEDICINE
(2023)
Article
Biology
Sang Hwa Kim, Kye D. Nichols, Eric N. Anderson, Yining Liu, Nandini Ramesh, Weiyan Jia, Connor J. Kuerbis, Mark Scalf, Lloyd M. Smith, Udai Bhan Pandey, Randal S. Tibbetts, Jeannie Chin
Summary: Mutations in UBQLN2 cause X-linked forms of ALS and FTD, but the underlying mechanisms are unknown. Studying ALS-associated mutants of UBQLN2 in Drosophila, it was found that they trigger heat stress-dependent neurodegeneration. A genetic modifier screen identified endolysosomal and axon guidance genes, including the netrin receptor Unc-5, as key regulators of UBQLN2 toxicity. Reduced dosage of Unc-5 or its coreceptor Dcc/frazzled alleviated neurodegenerative phenotypes in flies expressing UBQLN2(ALS) alleles. Further experiments using iPSCs and iMNs demonstrated lysosomal defects and cytosolic UBQLN2 inclusions, neurite complexity reduction, and growth cone defects, which were partially reversed by silencing of UNC5B and DCC. These findings suggest altered growth cone dynamics as a conserved pathomechanism in UBQLN2-associated ALS/FTD.
Article
Biochemistry & Molecular Biology
Qiankun Liu, Pengtao Li, Shuang Cheng, Zilin Zhao, Yuling Liu, Yangyang Wei, Quanwei Lu, Jiangping Han, Xiaoyan Cai, Zhongli Zhou, Muhammad Jawad Umer, Renhai Peng, Baohong Zhang, Fang Liu
Summary: This study developed a method for single-cell RNA-seq based on isolating protoplast from cotton root tips and investigated the impact of salinity stress on gene expression. The results revealed many differentially expressed genes related to stress response and cellular metabolism after salt treatment. Additionally, salinity-responsive genes involved in plant hormone signaling and MAPK signaling were identified, as well as transcription factors associated with salt stress response.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Pawandeep Singh Kohli, Lekha T. Pazhamala, Balaji Mani, Jitendra Kumar Thakur, Jitender Giri
Summary: Root hairs are extensions of root epidermal cells that increase in length and density under low phosphorus availability. This study explores the genes involved in root hair development and response to low phosphorus in chickpea, an important leguminous crop. The findings reveal that genes related to root hair initiation and cellular differentiation are upregulated, and genes involved in cell wall synthesis, cytoskeleton/vesicle transport, and ethylene biosynthesis are also upregulated in root hairs. In addition, genes related to low phosphorus responses, such as lipid and/or pectin P remobilization and acid phosphatases, are induced in root hairs. The study also highlights the preferential enrichment of processes involved in symbiotic interactions in root hairs. Overall, root hairs exhibit a multifaceted response to low phosphorus, involving molecular changes in epidermal cell differentiation and root hair initiation, as well as tip growth and various low phosphorus responses in elongated root hairs.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Clinical Neurology
Josette J. Wlaschin, Caroline Donahue, Jacob Gluski, Jennifer F. Osborne, Leana M. Ramos, Hanna Silberberg, Claire E. Le Pichon
Summary: Wlaschin et al. demonstrate that combining DLK deletion to delay neuronal death with ATF3 expression to promote regeneration effectively preserves motor neuron function in a mouse model of ALS. This study provides evidence for potential combinatorial therapies for ALS and other motor diseases.
Article
Microbiology
Tiantian Wang, Xiaobin Li, Chunlan Zhang, Jize Xu
Summary: Green mold caused by Trichoderma spp. is a serious disease for the production of Ganoderma lingzhi. In this study, we identified differentially expressed genes (DEGs) in G. lingzhi at different time points after T. hengshanicum infection using RNA-seq and DGE profiling methods. We found that resistance-related genes were up-regulated, while heat shock protein (HSP) genes were down-regulated. Pathway enrichment analysis revealed enrichment of sphingolipid metabolism, ether lipid metabolism, and valine, leucine and isoleucine degradation pathway in G. lingzhi after infection. These findings contribute to the understanding of G. lingzhi defense against Trichoderma spp. and the development of strategies for disease control.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Rongfa Chen, Yegeng Fan, Huiwen Zhou, Shanping Mo, Zhongfeng Zhou, Haifeng Yan, Ting Luo, Xing Huang, Mengling Weng, Prakash Lakshmanan, Yangrui Li, Lihang Qiu, Jianming Wu
Summary: By obtaining high-quality long transcripts from sugarcane using the PacBio Sequel System, it was found that the inhibitory effects of DPC on plant growth may involve pathways related to plant hormone signal transduction and biosynthesis of several metabolites.
Article
Biochemistry & Molecular Biology
Paula Sancho, Luca Bartesaghi, Olivia Miossec, Francisco Garcia-Garcia, Laura Ramirez-Jimenez, Anna Siddell, Elisabet Akesson, Eva Hedlund, Petra Lassuthova, Samuel I. Pascual-Pascual, Teresa Sevilla, Marina Kennerson, Vincenzo Lupo, Roman Chrast, Carmen Espinos
HUMAN MOLECULAR GENETICS
(2019)
Article
Multidisciplinary Sciences
Phillip T. Newton, Lei Li, Baoyi Zhou, Christoph Schweingruber, Maria Hovorakova, Meng Xie, Xiaoyan Sun, Lakshmi Sandhow, Artem V. Artemov, Evgeny Ivashkin, Simon Suter, Vyacheslav Dyachuk, Maha El Shahawy, Amel Gritli-Linde, Thibault Bouderlique, Julian Petersen, Annelie Mollbrink, Joakim Lundeberg, Grigori Enikolopov, Hong Qian, Kaj Fried, Maria Kasper, Eva Hedlund, Igor Adameyko, Lars Savendahl, Andrei S. Chagin
Article
Clinical Neurology
M. Nizzardo, M. Taiana, F. Rizzo, J. Aguila Benitez, J. Nijssen, I Allodi, V Melzi, N. Bresolin, G. P. Comi, E. Hedlund, S. Corti
ACTA NEUROPATHOLOGICA
(2020)
Article
Neurosciences
Filipa Boucanova, Gill Pollmeier, Katalin Sandor, Carlos Morado Urbina, Jik Nijssen, Jean-Jacques Medard, Luca Bartesaghi, Luc Pellerin, Camilla Svensson, Eva Hedlund, Roman Chrast
Summary: Recent studies have shown that MCT1 in Schwann cells is necessary for maintaining the integrity of motor end-plates, while MCT4 appears largely dispensable for supporting motor neurons. Structural alterations and transcriptional changes in lumbar motor neurons from MCT1 cKO mice provide further insight into the biology of axon-glia metabolic crosstalk.
Article
Multidisciplinary Sciences
Daniel W. Hagey, Danijal Topcic, Nigel Kee, Florie Reynaud, Maria Bergsland, Thomas Perlmann, Jonas Muhr
NATURE COMMUNICATIONS
(2020)
Article
Cell Biology
Ahmed M. Osman, Ying Sun, Terry C. Burns, Liqun He, Nigel Kee, Nuria Oliva-Vilarnau, Androniki Alevyzaki, Kai Zhou, Lauri Louhivuori, Per Uhlen, Eva Hedlund, Christer Betsholtz, Volker M. Lauschke, Julianna Kele, Klas Blomgren
Article
Biochemistry & Molecular Biology
Susanne Nichterwitz, Jik Nijssen, Helena Storvall, Christoph Schweingruber, Laura Helen Comley, Ilary Allodi, Mirjam van der Lee, Qiaolin Deng, Rickard Sandberg, Eva Hedlund
Article
Multidisciplinary Sciences
Daniel Jutzi, Sebastien Campagne, Ralf Schmidt, Stefan Reber, Jonas Mechtersheimer, Foivos Gypas, Christoph Schweingruber, Martino Colombo, Christine von Schroetter, Fionna E. Loughlin, Anny Devoy, Eva Hedlund, Mihaela Zavolan, Frederic H. -T. Allain, Marc-David Ruepp
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Anna Manberg, Nathan Skene, Folkert Sanders, Marta Trusohamn, Julia Remnestal, Anna Szczepinska, Inci Sevval Aksoylu, Peter Lonnerberg, Lwaki Ebarasi, Stefan Wouters, Manuela Lehmann, Jennie Olofsson, Inti von Gohren Antequera, Aylin Domaniku, Maxim De Schaepdryver, Joke De Vocht, Koen Poesen, Mathias Uhlen, Jasper Anink, Caroline Mijnsbergen, Hermieneke Vergunst-Bosch, Annemarie Hubers, Ulf Klappe, Elena Rodriguez-Vieitez, Jonathan D. Gilthorpe, Eva Hedlund, Robert A. Harris, Eleonora Aronica, Philip Van Damme, Albert Ludolph, Jan Veldink, Caroline Ingre, Peter Nilsson, Sebastian A. Lewandowski
Summary: The study suggests that increased activity of perivascular fibroblast cells and vascular remodeling early in ALS pathogenesis can predict patient survival time. Elevated levels of SPP1 in plasma at disease diagnosis are a stronger predictor of shorter survival in ALS patients than established risk factors.
Article
Neurosciences
Julio Aguila, Shangli Cheng, Nigel Kee, Ming Cao, Menghan Wang, Qiaolin Deng, Eva Hedlund
Summary: This study identified transcriptomes and differentially expressed genes (DEGs) of human substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) dopamine neurons, revealing unique gene interactions and regulation differences between the subpopulations. Analysis of Parkinson's Disease tissues showed potential biomarkers, such as down-regulated SNc markers SLIT1 and ATP2A3, distinguishing SNc and VTA dopamine neurons. These findings provide insights into modulating dopamine neuron resilience and validating cell identity of stem cell-derived dopamine neurons.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2021)
Article
Cell Biology
Jorge C. Correia, Yildiz Kelahmetoglu, Paulo R. Jannig, Christoph Schweingruber, Dasha Shvaikovskaya, Liu Zhengye, Igor Cervenka, Naveen Khan, Michael Stec, Mariana Oliveira, Jik Nijssen, Vicente Martinez-Redondo, Serge Ducommun, Michele Azzolini, Johanna T. Lanner, Sandra Kleiner, Eva Hedlund, Jorge L. Ruas
Summary: Endurance exercise has various effects on skeletal muscle, including promoting vascularization, oxidative metabolism, fiber-type switching, and neuromuscular junction integrity. The characteristics of muscle fibers must be linked to the identity of the innervating motor neuron, which is influenced by muscle-derived neurturin (NRTN). The NRTN signaling pathway can induce shifts in motor neuron identity towards slower types, while also increasing capillary density and oxidative capacity in muscle fibers.
Review
Biology
Christoph Schweingruber, Eva Hedlund
Summary: ALS is a fatal disease characterized by the loss of particular neurons called motor neurons, leading to paralysis. The reasons for the vulnerability and resilience of different motor neurons in ALS are not fully understood. Multiple cell types are involved in the disease progression and contribute to the selective vulnerability of motor neurons.
Article
Cell Biology
Victoria Woschitz, Irene Mei, Eva Hedlund, Lyndsay M. Murray
Summary: This study provides insights into the selective vulnerability of motor neurons in SMA mouse models, revealing unique patterns of pathology across different models and identifying transcript groups that potentially contribute to motor neuron protection.