Article
Biochemistry & Molecular Biology
Taruna Pandey, Chinmay A. Kalluraya, Bingying Wang, Ting Xu, Xinya Huang, Shouhong Guang, Matthew D. Daugherty, Dengke K. Ma
Summary: Natural selection drives the acquisition of resilience traits in organisms to protect against adverse environments. Horizontal gene transfer (HGT) is an important mechanism for organisms to acquire novel traits, including those related to immunity, metabolism, and reproduction through interdomain HGT (iHGT) from bacteria. This study reveals that a nematode gene, rml-3, has been acquired through iHGT from bacteria and confers exoskeleton resilience and protection against environmental toxins in Caenorhabditis elegans. The findings suggest that iHGT of an ancient bacterial rml-3 homolog enabled L-rhamnose biosynthesis in nematodes, promoting cuticle integrity and organismal resilience to environmental stressors during evolution.
Article
Multidisciplinary Sciences
Abbas Ghaddar, Erick Armingol, Chau Huynh, Louis Gevirtzman, Nathan E. Lewis, Robert Waterston, Eyleen J. O'Rourke
Summary: Gene activity plays a crucial role in cell identity, intercellular communication, and multicellular organism functioning. In this study, we have generated a comprehensive single-cell atlas of gene activity in Caenorhabditis elegans, a fertile adult metazoan. Our dataset includes 180 distinct cell types and 19,657 expressed genes, and we have identified transcription factor expression profiles that determine cellular identity. Additionally, we have predicted thousands of intercellular interactions and experimentally validated some of the ligand-receptor pairs involved.
Article
Mathematics
Sihai Yang, Xian-Hua Han, Yen-Wei Chen
Summary: With the development of imaging technology, a large number of biological images with three-dimensional (3D) spatial, time, and spectral information have been obtained. However, there is still a lack of a complete framework for analyzing multidimensional bioimages. In this study, a framework was constructed to analyze a multidimensional dataset based on the WDDD biological image database, including image segmentation, registration, and analysis using GND-PCA. The results demonstrated the effectiveness of the method in identifying vital factors and building statistical models.
Article
Chemistry, Multidisciplinary
Loan Thi Ngo, Wen-Tse Huang, Ming-Hsien Chan, Ting-Yi Su, Chien-Hsiu Li, Michael Hsiao, Ru-Shi Liu
Summary: This study investigates the neurotoxicity of all-inorganic lead halide perovskite quantum dots (PeQDs) using Caenorhabditis elegans as a model organism. The results show that PeQDs accumulate mainly in the alimentary system and head region, causing a decrease in locomotor behaviors, pharyngeal pumping, brood decline, short lifespan, and abnormal issues in reproduction. Excessive reactive oxygen species formation is also observed. The neurotoxicity of PeQDs is explained by gene expression. This study provides an insight into the neurotoxicity of PeQDs and inspires the development of nontoxic PeQDs.
Article
Biochemistry & Molecular Biology
Sukesh Kumar Bajire, Sudeep D. Ghate, Shriya Shetty, Shukla Banerjee, R. Shyama Prasad Rao, Veena Shetty, Rajesh P. Shastry
Summary: By analyzing the protein-protein interaction network, specific genes related to biofilm production and quorum sensing-mediated virulence/secretion system were identified. The PPI network consisted of 160 nodes and 627 edges, with 13 hub proteins identified. In silico and in vitro experiments showed that curcumin could mimic AHL and inhibit the virulence factors and biofilm formation in P. aeruginosa. Moreover, curcumin was also effective in protecting C. elegans from the effects of P. aeruginosa PAO1. (c) 2023 Elsevier Inc. All rights reserved.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Cell Biology
Tingting Li, Xiaoyan Yang, Zhigang Feng, Wang Nie, Zhiyu Fang, Yan Zou
Summary: The study demonstrates that CATP-8/P5A ATPase regulates neuronal migration in Caenorhabditis elegans by controlling EGL-20/Wnt biogenesis, suggesting a conserved role in neural development in both worms and human cells. This highlights the significance of P5A ATPase in translocating Wnt proteins to the ER for proper processing and secretion.
Article
Genetics & Heredity
Kaustav Sengupta, Sovan Saha, Anup Kumar Halder, Piyali Chatterjee, Mita Nasipuri, Subhadip Basu, Dariusz Plewczynski
Summary: Protein function prediction is an important field in biology and computer science. A new method called PFP-GO is proposed for predicting protein function using information from multiple sources. Performance analysis shows that PFP-GO outperforms other existing methods. Additionally, the predicted top-ranked GO terms are checked through multilayer network propagation and their impact on the 3D structure of the genome is observed.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Juan Ling, Lingyu Li, Lifeng Lin, Hui Xie, Yixiong Zheng, Xiaorong Wan
Summary: In this study, the ACBP gene family in nine legume crops was comprehensively explored through genome-wide identification. The results showed high similarity in gene structure and conserved motifs among the ACBP orthologs of these legumes. However, subcellular localization, cis-acting elements, and interaction protein analyses revealed potentially different functions. These findings will contribute to a better understanding of the roles of ACBPs in legumes and inspire further research.
FRONTIERS IN GENETICS
(2023)
Article
Pharmacology & Pharmacy
Moonjung Hyun, Laxmi Rathor, Hye-Jin Kim, Taylor McElroy, Kwang Hyun Hwang, Stephanie Wohlgemuth, Shayla Curry, Rui Xiao, Christiaan Leeuwenburgh, Jeong-Doo Heo, Sung Min Han
Summary: The study compared the effects of BPA and its substitutes on nematodes and mammalian cells and found that these BPA alternatives also have detrimental effects on development, growth, reproduction, lifespan, and mitochondrial function.
Article
Automation & Control Systems
Xianke Dong, Pengfei Song, Xinyu Liu
Summary: A robotic system for automated microinjection of C. elegans has been developed, significantly improving injection speed and success rate. Experimental results show that the system is 23 times faster than traditional manual injection techniques and has a higher success rate.
IEEE TRANSACTIONS ON AUTOMATION SCIENCE AND ENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Ban-seok Kim, Alfredo V. Alcantara Jr, Je-Hyun Moon, Atsushi Higashitani, Nahoko Higashitani, Timothy Etheridge, Nathaniel J. Szewczyk, Colleen S. Deane, Christopher J. Gaffney, Akira Higashibata, Toko Hashizume, Kyoung-hye Yoon, Jin I. Lee
Summary: Although spaceflight is becoming more common, the effects of space microgravity on the human body are still unknown. This study used C. elegans to investigate the impact of space microgravity on worm body wall muscle. Results showed that space microgravity causes muscle atrophy in C. elegans, and similar effects were observed with acute nutritional deprivation and muscle disuse. The study also identified a gene called clp-4 that promotes muscle atrophy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Surojit Sural, Oliver Hobert
Summary: The sequencing of the genome of the nematode Caenorhabditis elegans revealed an abundance of C4-zinc finger orphan nuclear hormone receptors, with most being an expansion of the HNF4-subtype. Despite most receptors having predicted ligand binding domains, no ligand has been identified for any of the non-conserved genes.
Article
Environmental Sciences
Huijie Li, Hao Li, Ning Zuo, Yi Liu, Di Lang, Christian Steinberg, Bo Pan, Baoshan Xing
Summary: Environmentally persistent free radicals (EPFRs) have attracted extensive attention due to their potential toxicity. In this study, the direct toxicity of EPFRs was confirmed by comparing systems without EPFRs, and it was found that EPFRs-containing particles exhibited significant toxicity to Caenorhabditis elegans (C. elegans), while the parent chemical and intermediate degradation products did not. EPFRs mediated the generation of reactive oxygen species and increased gene expressions related to oxidative stress, biotransformation, energy homeostasis, survival, proliferation, cell and embryonic development in C. elegans.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemical Research Methods
Hongxiao Wang, Hao Zheng, Danny Z. Chen
Summary: In this paper, the researchers propose a new framework called TANGO for predicting protein semantic similarities. The framework takes into consideration the taxonomy relations between GO terms and the different contributions of GO terms in describing protein semantics, leading to more accurate measurement of shared meanings between protein attributes.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Neurosciences
Adam J. Iliff, Can Wang, Elizabeth A. Ronan, Alison E. Hake, Yuling Guo, Xia Li, Xinxing Zhang, Maohua Zheng, Jianfeng Liu, Karl Grosh, R. Keith Duncan, X. Z. Shawn Xu
Summary: The ability to sense airborne sound extends beyond vertebrates and arthropods to include invertebrates as well, suggesting convergent evolution of auditory capabilities in the animal kingdom. The discovery challenges the conventional view that invertebrates are insensitive to sound and highlights the unexpected role of nAChRs in mechanosensation. Animals without ears should not be automatically presumed to be sound insensitive.
Editorial Material
Biochemistry & Molecular Biology
Silvia Dossena, Angela Marino
Article
Biochemistry & Molecular Biology
Markus Kwik, Stefan Hainzl, Jan Oppelt, Boris Tichy, Ulrich Koller, Emanuele Bernardinelli, Markus Steiner, Greta Zara, Charity Nofziger, Serge Weis, Markus Paulmichl, Silvia Dossena, Wolfgang Patsch, Selma M. Soyal
Summary: The study focuses on the transcriptional regulator PGC-1 alpha, with specific isoforms expressed in the CNS having distinct functional differences compared to reference proteins. Activation of the CNS promoter led to more differentially expressed genes compared to the reference promoter, while alternative exon usage was similar. The distinct N-terminal regions and shared downstream regions of PGC-1 alpha isoforms influence exon usage of multiple genes, with implications for neurodegenerative diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Physiology
Alessia Remigante, Sara Spinelli, Michael Pusch, Antonio Sarikas, Rossana Morabito, Angela Marino, Silvia Dossena
Summary: Bicarbonate, a major anion in mammalian tissues and fluids, plays a critical role in cell and systemic pH homeostasis and is involved in transporting ions and substrates across cell membranes. Chloride/bicarbonate exchangers, abundant in erythrocytes and epithelial cells, are particularly susceptible to oxidative stress. This review focuses on the physiological functions and pathophysiological changes of Cl-/HCO3- exchangers belonging to the SLC4 and SLC26 superfamilies in relation to oxidative stress.
Article
Biochemistry & Molecular Biology
Alessia Remigante, Sara Spinelli, Nancy Basile, Daniele Caruso, Giuseppe Falliti, Silvia Dossena, Angela Marino, Rossana Morabito
Summary: This study aimed to verify the protective role of Quercetin in a d-Galactose-induced model of aging in human erythrocytes. It was found that Quercetin preferentially improved lipid peroxidation rather than protein oxidation and prevented glycated hemoglobin formation. These findings suggest that the Band 3 protein could be a potential target for antioxidant treatments against aging-related disturbances.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Alessia Remigante, Sara Spinelli, Elisabetta Straface, Lucrezia Gambardella, Daniele Caruso, Giuseppe Falliti, Silvia Dossena, Angela Marino, Rossana Morabito
Summary: Aging is a decline in physiological functions, closely related to oxidative stress (OS). Functional foods rich in flavonoids are effective in counteracting age-related changes. This study confirmed the protective role of Aca extract in a model of aging in human erythrocytes, reducing OS damage and restoring protein distribution alterations.
Article
Biochemistry & Molecular Biology
Alessia Remigante, Sara Spinelli, Elisabetta Straface, Lucrezia Gambardella, Daniele Caruso, Giuseppe Falliti, Silvia Dossena, Angela Marino, Rossana Morabito
Summary: This study aims to investigate the response of red blood cells to oxidative stress and evaluate the potential beneficial effects of the natural antioxidant quercetin. The results indicate that pre-treatment with quercetin is more effective in protecting red blood cells against oxidative stress and preventing damage.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Neurosciences
Emanuele Bernardinelli, Sebastian Roesch, Edi Simoni, Angela Marino, Gerd Rasp, Laura Astolfi, Antonio Sarikas, Silvia Dossena
Summary: POU3F4 gene mutations are the main cause of X-linked deafness, resulting in hearing loss through impaired transcriptional activity and subcellular distribution. Using RNA sequencing and genetic analysis, researchers found that POU3F4 regulates the transcriptional levels of the amino acid transporter gene SLC6A20, providing insights into the mechanism of POU3F4-related deafness.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2022)
Article
Medicine, General & Internal
Arnoldas Matulevicius, Emanuele Bernardinelli, Zippora Brownstein, Sebastian Roesch, Karen B. Avraham, Silvia Dossena
Summary: The SLC26A4 gene mutation is associated with hearing loss and is particularly common in the Ashkenazi Jewish population. Cell-based assays confirmed that the mutant protein has reduced ion transport function, abnormal subcellular localization, and decreased expression levels, supporting its pathogenicity. Mouse experiments further demonstrated the relevance of this protein variant to Pendred syndrome/DFNB4.
JOURNAL OF CLINICAL MEDICINE
(2022)
Editorial Material
Cell Biology
Alessia Remigante, Paola Gavazzo, Rossana Morabito, Silvia Dossena
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Alessia Remigante, Sara Spinelli, Angela Marino, Michael Pusch, Rossana Morabito, Silvia Dossena
Summary: Oxidative stress and immune response are important factors in the development of cancers, including melanoma. Ion channels, which are aberrantly expressed in tumor cells, play a role in neoplastic transformation, malignant progression, and resistance to therapy. These ion channels, located in cellular membranes, are targets of oxidative stress, which is particularly elevated in melanoma. They also represent promising targets for therapeutic intervention in melanoma.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Andreas Konopa, Melanie A. Meier, Miriam J. Franz, Emanuele Bernardinelli, Anna-Lena Voegele, Raja Atreya, Silvia Ribback, Stephanie Roessler, Achim Aigner, Kerstin Singer, Stephan Singer, Antonio Sarikas, Susanne Muehlich
Summary: MRTF-A and MRTF-B are coactivators that regulate fundamental biological processes such as cell growth, migration, and differentiation. In hepatocellular carcinoma (HCC), MRTF and SRF activity play a crucial role. This study identifies the G protein-coupled lysophosphatidic acid receptor 1 (LPAR1) as a novel interaction partner of MRTF-A and Filamin A (FLNA), and reveals the potential therapeutic value of inhibiting the LPAR1-FLNA-MRTF-A interaction in HCC therapy.
Review
Biochemistry & Molecular Biology
Emanuele Bernardinelli, Florian Huber, Sebastian Roesch, Silvia Dossena
Summary: X-linked deafness (DFNX) accounts for up to 2% of hereditary hearing loss cases and can occur in syndromic and non-syndromic forms. POU3F4 is the most common gene associated with X-linked deafness and is responsible for about 50% of non-syndromic cases. It plays a crucial role in the development of the middle and inner ear. This article provides an overview of the pathogenic gene variants of POU3F4, discusses the clinical features, and highlights the importance of further research on its transcriptional targets in the ear and brain.
Review
Audiology & Speech-Language Pathology
Sebastian Roesch, Gerd Rasp, Antonio Sarikas, Silvia Dossena
Summary: Hearing loss is a common sensory deficit in humans, with at least 60% of cases in developed countries being of genetic origin. Enlarged vestibular aqueduct (EVA) is a commonly detected inner ear malformation associated with genetic hearing loss. Genes such as SLC26A4 and FOXI1 play a role in both non-syndromic and syndromic forms of EVA-related hearing loss.
AUDIOLOGY RESEARCH
(2021)