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Lee BH, Cevizci M, Lieblich SE, Ibrahim M, Wen Y, Eid RS, Lamers Y, Duarte-Guterman P, Galea LAM. Exploring the parity paradox: Differential effects on neuroplasticity and inflammation by APOEe4 genotype at middle age. Brain Behav Immun 2024; 120:54-70. [PMID: 38772427 DOI: 10.1016/j.bbi.2024.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 04/20/2024] [Accepted: 05/18/2024] [Indexed: 05/23/2024] Open
Abstract
Female sex and Apolipoprotein E (APOE) ε4 genotype are top non-modifiable risk factors for Alzheimer's disease (AD). Although female-unique experiences like parity (pregnancy and motherhood) have positive effects on neuroplasticity at middle age, previous pregnancy may also contribute to AD risk. To explore these seemingly paradoxical long-term effects of parity, we investigated the impact of parity with APOEε4 genotype by examining behavioural and neural biomarkers of brain health in middle-aged female rats. Our findings show that primiparous (parous one time) hAPOEε4 rats display increased use of a non-spatial cognitive strategy and exhibit decreased number and recruitment of new-born neurons in the ventral dentate gyrus of the hippocampus in response to spatial working memory retrieval. Furthermore, primiparity and hAPOEε4 genotype synergistically modulate inflammatory markers in the ventral hippocampus. Collectively, these findings demonstrate that previous parity in hAPOEε4 rats confers an added risk to present with reduced activity and engagement of the hippocampus as well as elevated pro-inflammatory signaling, and underscore the importance of considering female-specific factors and genotype in health research.
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Affiliation(s)
- Bonnie H Lee
- Graduate Program in Neuroscience, University of British Columbia, Vancouver, BC, Canada; Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada; Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Melike Cevizci
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada; Department of Psychology, University of British Columbia, Vancouver, BC, Canada
| | - Stephanie E Lieblich
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada; Department of Psychology, University of British Columbia, Vancouver, BC, Canada
| | - Muna Ibrahim
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada; Department of Psychology, University of British Columbia, Vancouver, BC, Canada
| | - Yanhua Wen
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada; Department of Psychology, University of British Columbia, Vancouver, BC, Canada
| | - Rand S Eid
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Yvonne Lamers
- Food Nutrition and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada
| | - Paula Duarte-Guterman
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada; Department of Psychology, University of British Columbia, Vancouver, BC, Canada
| | - Liisa A M Galea
- Graduate Program in Neuroscience, University of British Columbia, Vancouver, BC, Canada; Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada; Department of Psychology, University of British Columbia, Vancouver, BC, Canada; Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada; Department of Psychiatry, University of Toronto, ON, Canada.
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2
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De Meulemeester AS, Reid C, Auvin S, Carlen PL, Cole AJ, Szlendak R, Di Sapia R, Moshé SL, Sankar R, O'Brien TJ, Baulac S, Henshall DC, Akman Ö, Galanopoulou AS. WONOEP appraisal: Modeling early onset epilepsies. Epilepsia 2024. [PMID: 39042520 DOI: 10.1111/epi.18063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/25/2024]
Abstract
Epilepsy has a peak incidence during the neonatal to early childhood period. These early onset epilepsies may be severe conditions frequently associated with comorbidities such as developmental deficits and intellectual disability and, in a significant percentage of patients, may be medication-resistant. The use of adult rodent models in the exploration of mechanisms and treatments for early life epilepsies is challenging, as it ignores significant age-specific developmental differences. More recently, models developed in immature animals, such as rodent pups, or in three-dimensional organoids may more closely model aspects of the immature brain and could result in more translatable findings. Although models are not perfect, they may offer a more controlled screening platform in studies of mechanisms and treatments, which cannot be done in pediatric patient cohorts. On the other hand, more simplified models with higher throughput capacities are required to deal with the large number of epilepsy candidate genes and the need for new treatment options. Therefore, a combination of different modeling approaches will be beneficial in addressing the unmet needs of pediatric epilepsy patients. In this review, we summarize the discussions on this topic that occurred during the XVI Workshop on Neurobiology of Epilepsy, organized in 2022 by the Neurobiology Commission of the International League Against Epilepsy. We provide an overview of selected models of early onset epilepsies, discussing their advantages and disadvantages. Heterologous expression models provide initial functional insights, and zebrafish, rodent models, and brain organoids present increasingly complex platforms for modeling and validating epilepsy-related phenomena. Together, these models offer valuable insights into early onset epilepsies and accelerate hypothesis generation and therapy discovery.
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Affiliation(s)
- Ann-Sofie De Meulemeester
- Institut du Cerveau-Paris Brain Institute-ICM, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS, Sorbonne Université, Paris, France
- Laboratory for Molecular Biodiscovery, KU Leuven, Leuven, Belgium
| | - Christopher Reid
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
- Department of Medicine, Epilepsy Research Centre, Austin Health, University of Melbourne, Heidelberg, Victoria, Australia
| | - Stéphane Auvin
- Pediatric Neurology Department, CRMR Épilepsies Rares, EpiCARE member, AP-HP, Robert-Debré University Hospital, Paris, France
- INSERM NeuroDiderot, Université Paris Cité, Paris, France
- Institut Universitaire de France, Paris, France
| | - Peter L Carlen
- Krembil Research Institute, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Medicine and Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Andrew J Cole
- MGH Epilepsy Service, Division of Clinical Neurophysiology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Roza Szlendak
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
- Institut de Génomique Fonctionnelle, University of Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier, France
| | - Rossella Di Sapia
- Department of Acute Brain and Cardiovascular Injury, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Solomon L Moshé
- Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, USA
- Isabelle Rapin Division of Child Neurology, Albert Einstein College of Medicine, Bronx, New York, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Raman Sankar
- Department of Neurology and Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Terence J O'Brien
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Hospital, Melbourne, Victoria, Australia
| | - Stéphanie Baulac
- Institut du Cerveau-Paris Brain Institute-ICM, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS, Sorbonne Université, Paris, France
| | - David C Henshall
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland (RCSI) University of Medicine and Health Sciences, Dublin, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland (RCSI) University of Medicine and Health Sciences, Dublin, Ireland
| | - Özlem Akman
- Department of Physiology, Faculty of Medicine, Demiroglu Bilim University, Istanbul, Turkey
| | - Aristea S Galanopoulou
- Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, USA
- Isabelle Rapin Division of Child Neurology, Albert Einstein College of Medicine, Bronx, New York, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
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3
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Moldovan JB, Kopera HC, Liu Y, Garcia-Canadas M, Catalina P, Leone P, Sanchez L, Kitzman J, Kidd J, Garcia-Perez J, Moran J. Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes. Nucleic Acids Res 2024; 52:7761-7779. [PMID: 38850156 PMCID: PMC11260458 DOI: 10.1093/nar/gkae448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/10/2024] Open
Abstract
Alu elements are non-autonomous Short INterspersed Elements (SINEs) derived from the 7SL RNA gene that are present at over one million copies in human genomic DNA. Alu mobilizes by a mechanism known as retrotransposition, which requires the Long INterspersed Element-1 (LINE-1) ORF2-encoded protein (ORF2p). Here, we demonstrate that HeLa strains differ in their capacity to support Alu retrotransposition. Human Alu elements retrotranspose efficiently in HeLa-HA and HeLa-CCL2 (Alu-permissive) strains, but not in HeLa-JVM or HeLa-H1 (Alu-nonpermissive) strains. A similar pattern of retrotransposition was observed for other 7SL RNA-derived SINEs and tRNA-derived SINEs. In contrast, mammalian LINE-1s, a zebrafish LINE, a human SINE-VNTR-Alu (SVA) element, and an L1 ORF1-containing mRNA can retrotranspose in all four HeLa strains. Using an in vitro reverse transcriptase-based assay, we show that Alu RNAs associate with ORF2p and are converted into cDNAs in both Alu-permissive and Alu-nonpermissive HeLa strains, suggesting that 7SL- and tRNA-derived SINEs use strategies to 'hijack' L1 ORF2p that are distinct from those used by SVA elements and ORF1-containing mRNAs. These data further suggest ORF2p associates with the Alu RNA poly(A) tract in both Alu-permissive and Alu-nonpermissive HeLa strains, but that Alu retrotransposition is blocked after this critical step in Alu-nonpermissive HeLa strains.
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Affiliation(s)
- John B Moldovan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huira C Kopera
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ying Liu
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marta Garcia-Canadas
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada 18016, Spain
| | | | - Paola E Leone
- Genetics and Genomics Laboratory, SOLCA Hospital, Quito, Ecuador
| | - Laura Sanchez
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada 18016, Spain
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jose Luis Garcia-Perez
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada 18016, Spain
| | - John V Moran
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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Song B, Bae S. Genome editing using CRISPR, CAST, and Fanzor systems. Mol Cells 2024; 47:100086. [PMID: 38909984 PMCID: PMC11278801 DOI: 10.1016/j.mocell.2024.100086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/14/2024] [Accepted: 06/18/2024] [Indexed: 06/25/2024] Open
Abstract
Genetic engineering technologies are essential not only for basic science but also for generating animal models for therapeutic applications. The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) system, derived from adapted prokaryotic immune responses, has led to unprecedented advancements in the field of genome editing because of its ability to precisely target and edit genes in a guide RNA-dependent manner. The discovery of various types of CRISPR-Cas systems, such as CRISPR-associated transposons (CASTs), has resulted in the development of novel genome editing tools. Recently, research has expanded to systems associated with obligate mobile element guided activity (OMEGA) RNAs, including ancestral CRISPR-Cas and eukaryotic Fanzor systems, which are expected to complement the conventional CRISPR-Cas systems. In this review, we briefly introduce the features of various CRISPR-Cas systems and their application in diverse animal models.
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Affiliation(s)
- Beomjong Song
- Department of Anatomy, College of Medicine, Soonchunhyang University, Cheonan 33151, Republic of Korea.
| | - Sangsu Bae
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Medical Research Center of Genomic Medicine Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea.
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5
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Calamari ZT, Song A, Cohen E, Akter M, Roy RD, Hallikas O, Christensen MM, Li P, Marangoni P, Jernvall J, Klein OD. Vole genomics links determinate and indeterminate growth of teeth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.18.572015. [PMID: 38187646 PMCID: PMC10769287 DOI: 10.1101/2023.12.18.572015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Continuously growing teeth are an important innovation in mammalian evolution, yet genetic regulation of continuous growth by stem cells remains incompletely understood. Dental stem cells responsible for tooth crown growth are lost at the onset of tooth root formation. Genetic signaling that initiates this loss is difficult to study with the ever-growing incisor and rooted molars of mice, the most common mammalian dental model species, because signals for root formation overlap with signals that pattern tooth size and shape (i.e., cusp patterns). Different species of voles (Cricetidae, Rodentia, Glires) have evolved rooted and unrooted molars that have similar size and shape, providing alternative models for studying roots. We assembled a de novo genome of Myodes glareolus, a vole with high-crowned, rooted molars, and performed genomic and transcriptomic analyses in a broad phylogenetic context of Glires (rodents and lagomorphs) to assess differential selection and evolution in tooth forming genes. We identified 15 dental genes with changing synteny relationships and six dental genes undergoing positive selection across Glires, two of which were undergoing positive selection in species with unrooted molars, Dspp and Aqp1. Decreased expression of both genes in prairie voles with unrooted molars compared to bank voles supports the presence of positive selection and may underlie differences in root formation. Bulk transcriptomics analyses of embryonic molar development in bank voles also demonstrated conserved patterns of dental gene expression compared to mice, with species-specific variation likely related to developmental timing and morphological differences between mouse and vole molars. Our results support ongoing evolution of dental genes across Glires, revealing the complex evolutionary background of convergent evolution for ever-growing molars.
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Affiliation(s)
- Zachary T. Calamari
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
- The Graduate Center, City University of New York, 365 Fifth Ave, New York, NY 10016, USA
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Andrew Song
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
- Cornell University, 616 Thurston Ave, Ithaca, NY 14853, USA
| | - Emily Cohen
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
- New York University College of Dentistry, 345 E 34th St, New York, NY 10010
| | - Muspika Akter
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
| | - Rishi Das Roy
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Outi Hallikas
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Mona M. Christensen
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Pengyang Li
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA 90048, USA
| | - Pauline Marangoni
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA 90048, USA
| | - Jukka Jernvall
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, FI-00014 Helsinki, Finland
| | - Ophir D. Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA 90048, USA
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6
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Jang SW, Kim YR, Han JH, Jang H, Choi HW. Generation of mouse and rat xenogeneic ovaries in vitro for production of mouse oocyte. Anim Cells Syst (Seoul) 2024; 28:303-314. [PMID: 38868077 PMCID: PMC11168328 DOI: 10.1080/19768354.2024.2363601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
The system forming ovarian follicles is developed to investigate in vitro folliculogenesis in a confined environment to obtain functional oocytes. Several studies have reported the successful generation of fully functional oocytes using mouse-induced pluripotent stem cells (iPSCs) and mouse female germline stem cells (fGSCs) as sources of stem cells for in vitro gametogenesis models. In addition, human oogonia have been generated through heterologous co-culture of differentiated human primordial germ cell-like cells (hPGCLCs) with mouse germline somatic cells, although oocyte formation remains challenging. Thus, studies on in vitro ovarian formation in other species are utilized as an introductory approach for in vitro mammalian gametogenesis by understanding the differences in culture systems between species and underlying mechanisms. In this study, we optimized the method of the entire oogenesis process from rat embryonic gonads. We identified well-maturated MII oocytes from rat gonads using our constructed method. Moreover, we generated the first successful in vitro reconstitution of xenogeneic follicles from mouse primordial germ cells (PGCs) and rat somatic cells. We also established an appropriate culture medium and incubation period for xenogeneic follicles. This method will be helpful in studies of xenogeneic follicular development and oocyte generation.
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Affiliation(s)
- Si Won Jang
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Ye Rim Kim
- Department of Animal Science, Jeonbuk National University, Jeonju, Republic of Korea
| | - Jae Ho Han
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Hoon Jang
- Department of Life Science, Jeonbuk National University, Jeonju, Republic of Korea
| | - Hyun Woo Choi
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
- Department of Animal Science, Jeonbuk National University, Jeonju, Republic of Korea
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Ukaegbu K, Foyle D, Luan X, Schneiderman E, Allen EP, Plemons J, Svoboda KKH. The effect of an antioxidant gel compared to chlorhexidine during the soft tissue healing process: An animal study. J Periodontol 2024. [PMID: 38830780 DOI: 10.1002/jper.23-0794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Prolonged inflammation and oxidative stress can impede healing. To enhance healing efficiency, many solutions have been employed. This is an in vivo study comparing chlorhexidine (CHX) to a commercial antioxidant gel (AO). METHODS Envelope flaps were created in the lower incisor gingival region of 60 Sprague-Dawley rats, and acellular dermal matrix (ADM) was inserted. Animals were randomly assigned to postsurgical treatment application of AO gel or 0.12% CHX twice daily. A control group received no postsurgical treatment. Data collected (before surgery, 24 h, and 72 h) included surgical images, tissue samples, and weights. Blinded scorers assessed images using a wound healing scale. Real-time polymerase chain reaction (RT-PCR) was used for gene expression of tumor necrosis factor-alpha (TNFα), interleukin-1 (IL-1), myeloperoxidase (MPO), and superoxide dismutase (SOD). RESULTS The AO group scored higher than the CHX and control groups in clinical evaluation (p < 0.05). At 24 h, TNFα expression was upregulated in the AO group compared to CHX (p = 0.027) and controls (p = 0.018). The AO group had significantly higher expression of antioxidant enzyme (SOD) at 24 h compared to CHX (p = 0.021). All animals lost weight in the first 24 h. Animals treated with AO or CHX regained more weight at 72 h than control animals (p = 0.034 and 0.003, respectively). CONCLUSION Animals treated with AO healed faster. AO led to earlier upregulation of TNFα and antioxidant enzyme SOD. We hypothesized that AO promoted an earlier inflammatory process while counteracting oxidative stress by increasing antioxidant responses via SOD.
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Affiliation(s)
- Kelechi Ukaegbu
- Department of Periodontology, Texas A&M School of Dentistry, Dallas, Texas, USA
| | - Deborah Foyle
- Department of Periodontology, Texas A&M School of Dentistry, Dallas, Texas, USA
| | - Xianghong Luan
- Department of Biomedical Sciences, Texas A&M School of Dentistry, Dallas, Texas, USA
- Department of Oral and Craniofacial Sciences, University of Rochester, Rochester, New York, USA
| | - Emet Schneiderman
- Department of Biomedical Sciences, Texas A&M School of Dentistry, Dallas, Texas, USA
| | - Edward P Allen
- Department of Periodontology, Texas A&M School of Dentistry, Dallas, Texas, USA
| | - Jacqueline Plemons
- Department of Periodontology, Texas A&M School of Dentistry, Dallas, Texas, USA
| | - Kathy K H Svoboda
- Department of Biomedical Sciences, Texas A&M School of Dentistry, Dallas, Texas, USA
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8
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Liang H, Wang Y, Liu F, Duan G, Long J, Jin Y, Chen S, Yang H. The Application of Rat Models in Staphylococcus aureus Infections. Pathogens 2024; 13:434. [PMID: 38921732 PMCID: PMC11206676 DOI: 10.3390/pathogens13060434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/10/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024] Open
Abstract
Staphylococcus aureus (S. aureus) is a major human pathogen and can cause a wide range of diseases, including pneumonia, osteomyelitis, skin and soft tissue infections (SSTIs), endocarditis, mastitis, bacteremia, and so forth. Rats have been widely used in the field of infectious diseases due to their unique advantages, and the models of S. aureus infections have played a pivotal role in elucidating their pathogenic mechanisms and the effectiveness of therapeutic agents. This review outlined the current application of rat models in S. aureus infections and future prospects for rat models in infectious diseases caused by S. aureus.
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Affiliation(s)
- Hongyue Liang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China; (H.L.); (F.L.); (G.D.); (J.L.); (Y.J.); (S.C.)
| | - Yadong Wang
- Department of Toxicology, Henan Center for Disease Control and Prevention, Zhengzhou 450016, China;
| | - Fang Liu
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China; (H.L.); (F.L.); (G.D.); (J.L.); (Y.J.); (S.C.)
| | - Guangcai Duan
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China; (H.L.); (F.L.); (G.D.); (J.L.); (Y.J.); (S.C.)
| | - Jinzhao Long
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China; (H.L.); (F.L.); (G.D.); (J.L.); (Y.J.); (S.C.)
| | - Yuefei Jin
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China; (H.L.); (F.L.); (G.D.); (J.L.); (Y.J.); (S.C.)
| | - Shuaiyin Chen
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China; (H.L.); (F.L.); (G.D.); (J.L.); (Y.J.); (S.C.)
| | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China; (H.L.); (F.L.); (G.D.); (J.L.); (Y.J.); (S.C.)
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9
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Moldovan JB, Kopera HC, Liu Y, Garcia-Canadas M, Catalina P, Leone PE, Sanchez L, Kitzman JO, Kidd JM, Garcia-Perez JL, Moran JV. Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592410. [PMID: 38746229 PMCID: PMC11092746 DOI: 10.1101/2024.05.03.592410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Alu elements are non-autonomous Short INterspersed Elements (SINEs) derived from the 7SL RNA gene that are present at over one million copies in human genomic DNA. Alu mobilizes by a mechanism known as retrotransposition, which requires the Long INterspersed Element-1 (LINE-1 or L1) ORF2 -encoded protein (ORF2p). Here, we demonstrate that HeLa strains differ in their capacity to support Alu retrotransposition. Human Alu elements retrotranspose efficiently in HeLa-HA and HeLa-CCL2 ( Alu -permissive) strains, but not in HeLa-JVM or HeLa-H1 ( Alu -nonpermissive) strains. A similar pattern of retrotransposition was observed for other 7SL RNA -derived SINEs and tRNA -derived SINEs. In contrast, mammalian LINE-1s, a zebrafish LINE, a human SINE-VNTR - Alu ( SVA ) element, and an L1 ORF1 -containing messenger RNA can retrotranspose in all four HeLa strains. Using an in vitro reverse transcriptase-based assay, we show that Alu RNAs associate with ORF2p and are converted into cDNAs in both Alu -permissive and Alu -nonpermissive HeLa strains, suggesting that 7SL - and tRNA -derived SINE RNAs use strategies to 'hijack' L1 ORF2p that are distinct from those used by SVA elements and ORF1 -containing mRNAs. These data further suggest ORF2p associates with the Alu RNA poly(A) tract in both Alu -permissive and Alu -nonpermissive HeLa strains, but that Alu retrotransposition is blocked after this critical step in Alu -nonpermissive HeLa strains.
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10
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Libby AE, Solt CM, Jackman MR, Sherk VD, Foright RM, Johnson GC, Nguyen TT, Breit MJ, Hulett N, Rudolph MC, Roberson PA, Wellberg EA, Jambal P, Scalzo RL, Higgins J, Kumar TR, Wierman ME, Pan Z, Shankar K, Klemm DJ, Moreau KL, Kohrt WM, MacLean PS. Effects of follicle-stimulating hormone on energy balance and tissue metabolic health after loss of ovarian function. Am J Physiol Endocrinol Metab 2024; 326:E626-E639. [PMID: 38536037 PMCID: PMC11208003 DOI: 10.1152/ajpendo.00400.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/29/2024] [Accepted: 03/20/2024] [Indexed: 05/01/2024]
Abstract
Loss of ovarian function imparts increased susceptibility to obesity and metabolic disease. These effects are largely attributed to decreased estradiol (E2), but the role of increased follicle-stimulating hormone (FSH) in modulating energy balance has not been fully investigated. Previous work that blocked FSH binding to its receptor in mice suggested this hormone may play a part in modulating body weight and energy expenditure after ovariectomy (OVX). We used an alternate approach to isolate the individual and combined contributions of FSH and E2 in mediating energy imbalance and changes in tissue-level metabolic health. Female Wistar rats were ovariectomized and given the gonadotropin releasing hormone (GnRH) antagonist degarelix to suppress FSH production. E2 and FSH were then added back individually and in combination for a period of 3 wk. Energy balance, body mass composition, and transcriptomic profiles of individual tissues were obtained. In contrast to previous studies, suppression and replacement of FSH in our paradigm had no effect on body weight, body composition, food intake, or energy expenditure. We did, however, observe organ-specific effects of FSH that produced unique transcriptomic signatures of FSH in retroperitoneal white adipose tissue. These included reductions in biological processes related to lipogenesis and carbohydrate transport. In addition, rats administered FSH had reduced liver triglyceride concentration (P < 0.001), which correlated with FSH-induced changes at the transcriptomic level. Although not appearing to modulate energy balance after loss of ovarian function in rats, FSH may still impart tissue-specific effects in the liver and white adipose tissue that might affect the metabolic health of those organs.NEW & NOTEWORTHY We find no effect of follicle-stimulating hormone (FSH) on energy balance using a novel model in which rats are ovariectomized, subjected to gonadotropin-releasing hormone antagonism, and systematically given back FSH by osmotic pump. However, tissue-specific effects of FSH on adipose tissue and liver were observed in this study. These include unique transcriptomic signatures induced by the hormone and a stark reduction in hepatic triglyceride accumulation.
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Affiliation(s)
- Andrew E Libby
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Claudia M Solt
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Matthew R Jackman
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Vanessa D Sherk
- Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
- Center for Scientific Review, National Institutes of Health, Bethesda, Maryland, United States
| | - Rebecca M Foright
- Department of Anatomy and Cell Biology, University of Kansas Medical Campus, Kansas City, Kansas, United States
| | - Ginger C Johnson
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Thi-Tina Nguyen
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Matthew J Breit
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Nicholas Hulett
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Michael C Rudolph
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Campus, Oklahoma City, Oklahoma, United States
| | - Paul A Roberson
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Elizabeth A Wellberg
- Stephenson Cancer Center, University of Oklahoma Health Sciences Campus, Oklahoma City, Oklahoma, United States
| | - Purevsuren Jambal
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Rebecca L Scalzo
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Janine Higgins
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - T Rajendra Kumar
- Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Margaret E Wierman
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Zhaoxing Pan
- Section of Endocrinology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Kartik Shankar
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Dwight J Klemm
- Cardiovascular Pulmonary Research Laboratory, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Kerrie L Moreau
- Division of Geriatric Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Wendy M Kohrt
- Division of Geriatric Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Paul S MacLean
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
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11
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Villani F, Guarracino A, Ward RR, Green T, Emms M, Pravenec M, Prins P, Garrison E, Williams RW, Chen H, Colonna V. Pangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575041. [PMID: 38260597 PMCID: PMC10802574 DOI: 10.1101/2024.01.10.575041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The HXB/BXH family of recombinant inbred rat strains is a unique genetic resource that has been extensively phenotyped over 25 years, resulting in a vast dataset of quantitative molecular and physiological phenotypes. We built a pangenome graph from 10x Genomics Linked-Read data for 31 recombinant inbred rats to study genetic variation and association mapping. The pangenome includes 0.2Gb of sequence that is not present the reference mRatBN7.2, confirming the capture of substantial additional variation. We validated variants in challenging regions, including complex structural variants resolving into multiple haplotypes. Phenome-wide association analysis of validated SNPs uncovered variants associated with glucose/insulin levels and hippocampal gene expression. We propose an interaction between Pirl1l1, chromogranin expression, TNF-α levels, and insulin regulation. This study demonstrates the utility of linked-read pangenomes for comprehensive variant detection and mapping phenotypic diversity in a widely used rat genetic reference panel.
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Affiliation(s)
- Flavia Villani
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Rachel R Ward
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center
| | - Tomomi Green
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center
| | - Madeleine Emms
- Institute of Genetics and Biophysics, National Research Council, Naples, 80111, Italy
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, 14200 Prague, Czech Republic
| | - Pjotr Prins
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Erik Garrison
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Robert W. Williams
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center
| | - Vincenza Colonna
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Institute of Genetics and Biophysics, National Research Council, Naples, 80111, Italy
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12
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de Jong TV, Pan Y, Rastas P, Munro D, Tutaj M, Akil H, Benner C, Chen D, Chitre AS, Chow W, Colonna V, Dalgard CL, Demos WM, Doris PA, Garrison E, Geurts AM, Gunturkun HM, Guryev V, Hourlier T, Howe K, Huang J, Kalbfleisch T, Kim P, Li L, Mahaffey S, Martin FJ, Mohammadi P, Ozel AB, Polesskaya O, Pravenec M, Prins P, Sebat J, Smith JR, Solberg Woods LC, Tabakoff B, Tracey A, Uliano-Silva M, Villani F, Wang H, Sharp BM, Telese F, Jiang Z, Saba L, Wang X, Murphy TD, Palmer AA, Kwitek AE, Dwinell MR, Williams RW, Li JZ, Chen H. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats. CELL GENOMICS 2024; 4:100527. [PMID: 38537634 PMCID: PMC11019364 DOI: 10.1016/j.xgen.2024.100527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/26/2023] [Accepted: 02/29/2024] [Indexed: 04/09/2024]
Abstract
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
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Affiliation(s)
- Tristan V de Jong
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Yanchao Pan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA
| | - Monika Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Chris Benner
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Denghui Chen
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - William Chow
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Wendy M Demos
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Peter A Doris
- The Brown Foundation Institute of Molecular Medicine, Center for Human Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Hakan M Gunturkun
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Victor Guryev
- Genome Structure and Ageing, University of Groningen, UMC, Groningen, the Netherlands
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Jun Huang
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ted Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA
| | - Panjun Kim
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ling Li
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Pejman Mohammadi
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jennifer R Smith
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hongyang Wang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Burt M Sharp
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Francesca Telese
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Laura Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
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13
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Castaño-González K, Köppl C, Pyott SJ. The crucial role of diverse animal models to investigate cochlear aging and hearing loss. Hear Res 2024; 445:108989. [PMID: 38518394 DOI: 10.1016/j.heares.2024.108989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/18/2024] [Accepted: 03/04/2024] [Indexed: 03/24/2024]
Abstract
Age-related hearing loss affects a large and growing segment of the population, with profound impacts on quality of life. Age-related pathology of the cochlea-the mammalian hearing organ-underlies age-related hearing loss. Because investigating age-related changes in the cochlea in humans is challenging and often impossible, animal models are indispensable to investigate these mechanisms as well as the complex consequences of age-related hearing loss on the brain and behavior. In this review, we advocate for a comparative and interdisciplinary approach while also addressing the challenges of comparing age-related hearing loss across species with varying lifespans. We describe the experimental advantages and limitations as well as areas for future research in well-established models of age-related hearing loss, including mice, rats, gerbils, chinchillas, and birds. We also indicate the need to expand characterization of age-related hearing loss in other established animal models, especially guinea pigs, cats, and non-human primates, in which auditory function is well characterized but age-related cochlear pathology is understudied. Finally, we highlight the potential of emerging animal models for advancing our understanding of age-related hearing loss, including deer mice, with their notably extended lifespans and preserved hearing, naked mole rats, with their exceptional longevity and extensive vocal communications, as well as zebrafish, which offer genetic tractability and suitability for drug screening. Ultimately, a comparative and interdisciplinary approach in auditory research, combining insights from various animal models with human studies, is key to robust and reliable research outcomes that better advance our understanding and treatment of age-related hearing loss.
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Affiliation(s)
- Karen Castaño-González
- Department of Otorhinolaryngology, Head & Neck Surgery, University Medical Center Groningen; The Research School of Behavioural and Cognitive Neurosciences, University of Groningen, Groningen, The Netherlands
| | - Christine Köppl
- Cluster of Excellence "Hearing4All", Department of Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky Universität; Research Center Neurosensory Science, Carl von Ossietzky Universität, Oldenburg, Germany
| | - Sonja J Pyott
- Department of Otorhinolaryngology, Head & Neck Surgery, University Medical Center Groningen; The Research School of Behavioural and Cognitive Neurosciences, University of Groningen, Groningen, The Netherlands.
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14
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Ma X, Xing Y, Zhai R, Du Y, Yan H. Development and advancements in rodent MRI-based brain atlases. Heliyon 2024; 10:e27421. [PMID: 38510053 PMCID: PMC10950579 DOI: 10.1016/j.heliyon.2024.e27421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/15/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Rodents, particularly mice and rats, are extensively utilized in fundamental neuroscience research. Brain atlases have played a pivotal role in this field, evolving from traditional printed histology atlases to digital atlases incorporating diverse imaging datasets. Magnetic resonance imaging (MRI)-based brain atlases, also known as brain maps, have been employed in specific studies. However, the existence of numerous versions of MRI-based brain atlases has impeded their standardized application and widespread use, despite the consensus within the academic community regarding their significance in mice and rats. Furthermore, there is a dearth of comprehensive and systematic reviews on MRI-based brain atlases for rodents. This review aims to bridge this gap by providing a comprehensive overview of the advancements in MRI-based brain atlases for rodents, with a specific focus on mice and rats. It seeks to explore the advantages and disadvantages of histologically printed brain atlases in comparison to MRI brain atlases, delineate the standardized methods for creating MRI brain atlases, and summarize their primary applications in neuroscience research. Additionally, this review aims to assist researchers in selecting appropriate versions of MRI brain atlases for their studies or refining existing MRI brain atlas resources, thereby facilitating the development and widespread adoption of standardized MRI-based brain atlases in rodents.
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Affiliation(s)
- Xiaoyi Ma
- Department of Geriatrics, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yao Xing
- School of Information Science and Technology, Fudan University, Shanghai, 200433, China
- Wuhan United Imaging Life Science Instrument Co., Ltd., Wuhan, 430071, China
| | - Renkuan Zhai
- Wuhan United Imaging Life Science Instrument Co., Ltd., Wuhan, 430071, China
| | - Yingying Du
- Wuhan United Imaging Life Science Instrument Co., Ltd., Wuhan, 430071, China
| | - Huanhuan Yan
- Shenzhen United Imaging Research Institute of Innovative Medical Equipment, Shenzhen, 518048, China
- Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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15
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Chen J, Jamaiyar A, Wu W, Hu Y, Zhuang R, Sausen G, Cheng HS, de Oliveira Vaz C, Pérez-Cremades D, Tzani A, McCoy MG, Assa C, Eley S, Randhawa V, Lee K, Plutzky J, Hamburg NM, Sabatine MS, Feinberg MW. Deficiency of lncRNA MERRICAL abrogates macrophage chemotaxis and diabetes-associated atherosclerosis. Cell Rep 2024; 43:113815. [PMID: 38428421 PMCID: PMC11006532 DOI: 10.1016/j.celrep.2024.113815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 01/18/2024] [Accepted: 02/01/2024] [Indexed: 03/03/2024] Open
Abstract
Diabetes-associated atherosclerosis involves excessive immune cell recruitment and plaque formation. However, the mechanisms remain poorly understood. Transcriptomic analysis of the aortic intima in Ldlr-/- mice on a high-fat, high-sucrose-containing (HFSC) diet identifies a macrophage-enriched nuclear long noncoding RNA (lncRNA), MERRICAL (macrophage-enriched lncRNA regulates inflammation, chemotaxis, and atherosclerosis). MERRICAL expression increases by 249% in intimal lesions during progression. lncRNA-mRNA pair genomic mapping reveals that MERRICAL positively correlates with the chemokines Ccl3 and Ccl4. MERRICAL-deficient macrophages exhibit lower Ccl3 and Ccl4 expression, chemotaxis, and inflammatory responses. Mechanistically, MERRICAL guides the WDR5-MLL1 complex to activate CCL3 and CCL4 transcription via H3K4me3 modification. MERRICAL deficiency in HFSC diet-fed Ldlr-/- mice reduces lesion formation by 74% in the aortic sinus and 86% in the descending aorta by inhibiting leukocyte recruitment into the aortic wall and pro-inflammatory responses. These findings unveil a regulatory mechanism whereby a macrophage-enriched lncRNA potently inhibits chemotactic responses, alleviating lesion progression in diabetes.
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Affiliation(s)
- Jingshu Chen
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anurag Jamaiyar
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Winona Wu
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yi Hu
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rulin Zhuang
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Cardiovascular Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Grasiele Sausen
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Henry S Cheng
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Camila de Oliveira Vaz
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Pérez-Cremades
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Physiology, University of Valencia and INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
| | - Aspasia Tzani
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael G McCoy
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Carmel Assa
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Samuel Eley
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vinay Randhawa
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jorge Plutzky
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Naomi M Hamburg
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA
| | - Marc S Sabatine
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mark W Feinberg
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Liao BY, Weng MP, Chang TY, Chang AYF, Ching YH, Wu CH. Degeneration of the Olfactory System in a Murid Rodent that Evolved Diurnalism. Mol Biol Evol 2024; 41:msae037. [PMID: 38376543 PMCID: PMC10906987 DOI: 10.1093/molbev/msae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/03/2024] [Accepted: 02/13/2024] [Indexed: 02/21/2024] Open
Abstract
In mammalian research, it has been debated what can initiate an evolutionary tradeoff between different senses, and the phenomenon of sensory tradeoff in rodents, the most abundant mammalian clade, is not evident. The Nile rat (Arvicanthis niloticus), a murid rodent, recently adapted to a diurnal niche through an evolutionary acquisition of daylight vision with enhanced visual acuity. As such, this model provides an opportunity for a cross-species investigation where comparative morphological and multi-omic analyses of the Nile rat are made with its closely related nocturnal species, e.g. the mouse (Mus musculus) and the rat (Rattus norvegicus). Thus, morphological examinations were performed, and evolutionary reductions in relative sizes of turbinal bone surfaces, the cribriform plate, and the olfactory bulb were discovered in Nile rats. Subsequently, we compared multiple murid genomes, and profiled olfactory epithelium transcriptomes of mice and Nile rats at various ages with RNA sequencing. The results further demonstrate that, in comparison with mouse olfactory receptor (OR) genes, Nile rat OR genes have experienced less frequent gain, more frequent loss, and more frequent expression reduction during their evolution. Furthermore, functional degeneration of coding sequences in the Nile rat lineage was found in OR genes, yet not in other genes. Taken together, these results suggest that acquisition of improved vision in the Nile rat has been accompanied by degeneration of both olfaction-related anatomical structures and OR gene repertoires, consistent with the hypothesis of an olfaction-vision tradeoff initiated by the switch from a nocturnal to a diurnal lifestyle in mammals.
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Affiliation(s)
- Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Meng-Pin Weng
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Ting-Yan Chang
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Andrew Ying-Fei Chang
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Yung-Hao Ching
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Taiwan, Republic of China
| | - Chia-Hwa Wu
- Laboratory Animal Center, National Health Research Institutes, Taiwan, Republic of China
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17
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Kawase M, Ichiyanagi K. Mouse retrotransposons: sequence structure, evolutionary age, genomic distribution and function. Genes Genet Syst 2024; 98:337-351. [PMID: 37989301 DOI: 10.1266/ggs.23-00221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Retrotransposons are transposable elements that are transposed via transcription and reverse transcription. Their copies have accumulated in the genome of mammals, occupying approximately 40% of mammalian genomic mass. These copies are often involved in numerous phenomena, such as chromatin spatial organization, gene expression, development and disease, and have been recognized as a driving force in evolution. Different organisms have gained specific retrotransposon subfamilies and retrotransposed copies, such as hundreds of Mus-specific subfamilies with diverse sequences and genomic locations. Despite this complexity, basic information is still necessary for present-day genomic and epigenomic studies. Herein, we describe the characteristics of each subfamily of Mus-specific retrotransposons in terms of sequence structure, phylogenetic relationships, evolutionary age, and preference for A or B compartments of chromatin.
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Affiliation(s)
- Masaki Kawase
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University
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18
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Gong W, Chen J, Xu S, Li Y, Zhou Y, Qin X. The regulatory effect of Angelicae Sinensis Radix on neuroendocrine-immune network and sphingolipid metabolism in CUMS-induced model of depression. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117217. [PMID: 37769886 DOI: 10.1016/j.jep.2023.117217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/03/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Conventional antidepressants therapy remains unsatisfactory due to the disadvantages of delayed clinical onset of action and side effects. Traditional Chinese Medicine (TCM) with good efficacy and higher safety have received much attention. Angelicae Sinensis Radix (AS), a well-known TCM, has been proved to exhibit the efficacy of antidepression recently. AIM OF THE STUDY The purpose of this study was to investigate the potential anti-depressant mechanisms of AS based on chronic unpredictable mild stress (CUMS) rat model. MATERIALS AND METHODS In this study, behavioral experiments, molecular biology techniques, and ultra performance liquid chromatography-triple-time of flight mass spectrometer (UPLC-Triple-TOF/MS) were combined to explore the potential antidepressant mechanisms of AS based on CUMS rat model. RESULTS The results demonstrated that AS could reduce the contents of serum hypothalamic-pituitary-adrenal (HPA) axis hormones in CUMS rats, including corticotropin-releasing hormone (CRH), adrenocorticotropic hormone (ACTH) and cortisol (CORT). In addition, AS regulated the percentage of CD4+ T lymphocytes, the ratio of CD4+/CD8+, and the levels of serum cytokines such as IL-1β, IL-4, IL-6, and TNF-α in CUMS rats. Lipidomics showed that 31 lipids were related to depression and AS could regulate the lipid metabolism alteration induced by CUMS, particularly sphingolipid metabolism. Finally, the key proteins in sphingolipid metabolic pathways in hippocampus of CUMS rats could be back-regulated by AS, including serine palmitoyl transferase (SPTLC2), ceramide synthase (CerS2), sphingomyelinase (SPHK1), and neutral sphingomyelinase (nSMase). CONCLUSION AS could alleviate NEI network disorder and restore the levels of sphingolipid metabolites and key proteins in CUMS rats. The underlying mechanism by which AS relieved depression-like behavior in CUMS rats may be through modulation of NEI and disturbances in sphingolipid metabolism.
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Affiliation(s)
- Wenxia Gong
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, China; Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, China; Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, China.
| | - Jinlong Chen
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, China
| | - Shaohua Xu
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, China
| | - Yuanji Li
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Opto-Electronics, Shanxi University, China
| | - Yuzhi Zhou
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, China; Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, China; Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, China
| | - Xuemei Qin
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, China; Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, China; Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, China.
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19
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Cai P, Zhang W, Jiang S, Xiong Y, Qiao H, Yuan H, Gao Z, Zhou Y, Jin S, Fu H. Role of Mn-LIPA in Sex Hormone Regulation and Gonadal Development in the Oriental River Prawn, Macrobrachium nipponense. Int J Mol Sci 2024; 25:1399. [PMID: 38338678 PMCID: PMC10855233 DOI: 10.3390/ijms25031399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
This study investigates the role of lysosomal acid lipase (LIPA) in sex hormone regulation and gonadal development in Macrobrachium nipponense. The full-length Mn-LIPA cDNA was cloned, and its expression patterns were analyzed using quantitative real-time PCR (qPCR) in various tissues and developmental stages. Higher expression levels were observed in the hepatopancreas, cerebral ganglion, and testes, indicating the potential involvement of Mn-LIPA in sex differentiation and gonadal development. In situ hybridization experiments revealed strong Mn-LIPA signaling in the spermatheca and hepatopancreas, suggesting their potential role in steroid synthesis (such as cholesterol, fatty acids, cholesteryl ester, and triglycerides) and sperm maturation. Increased expression levels of male-specific genes, such as insulin-like androgenic gland hormone (IAG), sperm gelatinase (SG), and mab-3-related transcription factor (Dmrt11E), were observed after dsMn-LIPA (double-stranded LIPA) injection, and significant inhibition of sperm development and maturation was observed histologically. Additionally, the relationship between Mn-LIPA and sex-related genes (IAG, SG, and Dmrt11E) and hormones (17β-estradiol and 17α-methyltestosterone) was explored by administering sex hormones to male prawns, indicating that Mn-LIPA does not directly control the production of sex hormones but rather utilizes the property of hydrolyzing triglycerides and cholesterol to provide energy while influencing the synthesis and secretion of self-sex hormones. These findings provide valuable insights into the function of Mn-LIPA in M. nipponense and its potential implications for understanding sex differentiation and gonadal development in crustaceans. It provides an important theoretical basis for the realization of a monosex culture of M. nipponense.
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Affiliation(s)
- Pengfei Cai
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (P.C.); (H.Y.); (Z.G.); (Y.Z.)
| | - Wenyi Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (W.Z.); (S.J.); (Y.X.); (H.Q.)
| | - Sufei Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (W.Z.); (S.J.); (Y.X.); (H.Q.)
| | - Yiwei Xiong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (W.Z.); (S.J.); (Y.X.); (H.Q.)
| | - Hui Qiao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (W.Z.); (S.J.); (Y.X.); (H.Q.)
| | - Huwei Yuan
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (P.C.); (H.Y.); (Z.G.); (Y.Z.)
| | - Zijian Gao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (P.C.); (H.Y.); (Z.G.); (Y.Z.)
| | - Yongkang Zhou
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (P.C.); (H.Y.); (Z.G.); (Y.Z.)
| | - Shubo Jin
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (P.C.); (H.Y.); (Z.G.); (Y.Z.)
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (W.Z.); (S.J.); (Y.X.); (H.Q.)
| | - Hongtuo Fu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (P.C.); (H.Y.); (Z.G.); (Y.Z.)
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (W.Z.); (S.J.); (Y.X.); (H.Q.)
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Li J, Huang E, Wu Y, Zhu C, Li W, Ai L, Xie Q, Tian Z, Zhong W, Sun G, Zhang L, Tan W. Population structure, dispersion patterns and genetic diversity of two major invasive and commensal zoonotic disease hosts ( Rattus norvegicus and Rattus tanezumi) from the southeastern coast of China. Front Genet 2024; 14:1174584. [PMID: 38259625 PMCID: PMC10800861 DOI: 10.3389/fgene.2023.1174584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Background: The invasive brownrat (Rattus norvegicus) and the Oriental rats (Rattus tanezumi) are common commensal murid that are important hosts for rodent-borne diseases in southeast Asia. Understanding their population structure and genetic diversity is essential to uncover their invasion biology and distribution dynamics that are essential for controlling rodent-borne diseases. Methods: TA total of 103 R. norvegicus and 85 R. tanezumi were collected from 13 to 9 coastal areas of six provincial monitoring sentinel sites, respectivelyto assess patterns in their microsatellite loci and their mitochondrial coxl gene region. Results: Eleven sampled populations of R. norvegicus were divided into two major clusters by region. The observed heterozygosity values of all regional populations were smaller than expected genetic diversity heterozygosity values and deviated from Hardy-Weinberg equilibrium Nine sample populations of R. tanezumi were divided into three clusters; two that included sample from Hainan and Fujian provinces, and one that included samples from the other provinces and cities. The genetic diversity of R. tanezumi was highest in samples from Jiangsu and Guangdong provinces. Conclusion: The data in this paper confirm the two invasive rodent species from the southeastern coastal region of China may have relied on maritime transport to spread from the southern region of China to the Yangtze River basin. R. tanezumi may then hanve migrated unidirectionally, along the southeastern provinces of China towards the north, while R. norvegicus spread in a complex and multidirectional manner in Hainan, Fujian, Zhejiang and Jiangsu Provinces of the country.
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Affiliation(s)
- Jiaqiao Li
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
- School of Resources and Chemical Engineering, Sanming University, Sanming, China
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Enjiong Huang
- Technology Center of Fuzhou Customs, Fuzhou, Fujian, China
| | - Yifan Wu
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Changqiang Zhu
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Wenhao Li
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Lele Ai
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Qinghua Xie
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhi Tian
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Weiwen Zhong
- Center for Disease Control and Prevention, Longquan, Zhejiang, China
| | - Gang Sun
- School of Resources and Chemical Engineering, Sanming University, Sanming, China
| | - Lingling Zhang
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weilong Tan
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
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21
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Summers KM. Genetic models of fibrillinopathies. Genetics 2024; 226:iyad189. [PMID: 37972149 PMCID: PMC11021029 DOI: 10.1093/genetics/iyad189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023] Open
Abstract
The fibrillinopathies represent a group of diseases in which the 10-12 nm extracellular microfibrils are disrupted by genetic variants in one of the genes encoding fibrillin molecules, large glycoproteins of the extracellular matrix. The best-known fibrillinopathy is Marfan syndrome, an autosomal dominant condition affecting the cardiovascular, ocular, skeletal, and other systems, with a prevalence of around 1 in 3,000 across all ethnic groups. It is caused by variants of the FBN1 gene, encoding fibrillin-1, which interacts with elastin to provide strength and elasticity to connective tissues. A number of mouse models have been created in an attempt to replicate the human phenotype, although all have limitations. There are also natural bovine models and engineered models in pig and rabbit. Variants in FBN2 encoding fibrillin-2 cause congenital contractural arachnodactyly and mouse models for this condition have also been produced. In most animals, including birds, reptiles, and amphibians, there is a third fibrillin, fibrillin-3 (FBN3 gene) for which the creation of models has been difficult as the gene is degenerate and nonfunctional in mice and rats. Other eukaryotes such as the nematode C. elegans and zebrafish D. rerio have a gene with some homology to fibrillins and models have been used to discover more about the function of this family of proteins. This review looks at the phenotype, inheritance, and relevance of the various animal models for the different fibrillinopathies.
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Affiliation(s)
- Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba QLD 4102, Australia
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22
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Varadi G. Mechanism of Analgesia by Gabapentinoid Drugs: Involvement of Modulation of Synaptogenesis and Trafficking of Glutamate-Gated Ion Channels. J Pharmacol Exp Ther 2024; 388:121-133. [PMID: 37918854 DOI: 10.1124/jpet.123.001669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023] Open
Abstract
Gabapentinoids have clinically been used for treating epilepsy, neuropathic pain, and several other neurologic disorders for >30 years; however, the definitive molecular mechanism responsible for their therapeutic actions remained uncertain. The conventional pharmacological observation regarding their efficacy in chronic pain modulation is the weakening of glutamate release at presynaptic terminals in the spinal cord. While the α2/δ-1 subunit of voltage-gated calcium channels (VGCCs) has been identified as the primary drug receptor for gabapentinoids, the lack of consistent effect of this drug class on VGCC function is indicative of a minor role in regulating this ion channel's activity. The current review targets the efficacy and mechanism of gabapentinoids in treating chronic pain. The discovery of interaction of α2/δ-1 with thrombospondins established this protein as a major synaptogenic neuronal receptor for thrombospondins. Other findings identified α2/δ-1 as a powerful regulator of N-methyl-D-aspartate receptor (NMDA) and alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor (AMPAR) by potentiating the synaptic expression, a putative pathophysiological mechanism of neuropathic pain. Further, the interdependent interactions between thrombospondin and α2/δ-1 contribute to chronic pain states, while gabapentinoid ligands efficaciously reverse such pain conditions. Gabapentin normalizes and even blocks NMDAR and AMPAR synaptic targeting and activity elicited by nerve injury. SIGNIFICANCE STATEMENT: Gabapentinoid drugs are used to treat various neurological conditions including chronic pain. In chronic pain states, gene expression of cacnα2/δ-1 and thrombospondins are upregulated and promote aberrant excitatory synaptogenesis. The complex trait of protein associations that involve interdependent interactions between α2/δ-1 and thrombospondins, further, association of N-methyl-D-aspartate receptor and alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor with the C-tail of α2/δ-1, constitutes a macromolecular signaling complex that forms the crucial elements for the pharmacological mode of action of gabapentinoids.
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Kobayashi E, Hakamata Y, Enosawa S, Shang KM, Komatsu H. Firefly Rats: Illuminating the Scientific Community in Transplantation Research. Cell Transplant 2024; 33:9636897231224174. [PMID: 38235662 PMCID: PMC10798091 DOI: 10.1177/09636897231224174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024] Open
Abstract
Fireflies produce light through luciferase-catalyzed reactions involving luciferin, oxygen, and adenosine triphosphate, distinct from other luminescent organisms. This unique feature has revolutionized molecular biology and physiology, serving as a valuable tool for cellular research. Luciferase-based bioluminescent imaging enabled the creation of transgenic animals, such as Firefly Rats. Firefly Rats, created in 2006, ubiquitously express luciferase and have become a critical asset in scientific investigations. These rats have significantly contributed to transplantation and tissue engineering studies. Their low immunogenicity reduces graft rejection risk, making them ideal for long-term tracking of organ/tissue/cellular engraftments. Importantly, in the islet transplantation setting, the ubiquitous luciferase expression in these rats does not alter islet morphology or function, ensuring accurate assessments of engrafted islets. Firefly Rats have illuminated the path of transplantation research worldwide for over a decade and continue accelerating scientific advancements in many fields.
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Affiliation(s)
- Eiji Kobayashi
- Department of Kidney Regenerative Medicine, The Jikei University School of Medicine, Tokyo, Japan
- Division of Basic Science, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Yoji Hakamata
- Division of Basic Science, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Shin Enosawa
- Department of Kidney Regenerative Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Kuang-Ming Shang
- Department of Medical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hirotake Komatsu
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA, USA
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Hartmann T, Middendorf M, Bernt M. Genome Rearrangement Analysis : Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches. Methods Mol Biol 2024; 2802:215-245. [PMID: 38819562 DOI: 10.1007/978-1-0716-3838-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Genome rearrangements are mutations that change the gene content of a genome or the arrangement of the genes on a genome. Several years of research on genome rearrangements have established different algorithmic approaches for solving some fundamental problems in comparative genomics based on gene order information. This review summarizes the literature on genome rearrangement analysis along two lines of research. The first line considers rearrangement models that are particularly well suited for a theoretical analysis. These models use rearrangement operations that cut chromosomes into fragments and then join the fragments into new chromosomes. The second line works with rearrangement models that reflect several biologically motivated constraints, e.g., the constraint that gene clusters have to be preserved. In this chapter, the border between algorithmically "easy" and "hard" rearrangement problems is sketched and a brief review is given on the available software tools for genome rearrangement analysis.
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Affiliation(s)
- Tom Hartmann
- Swarm Intelligence and Complex Systems Group, Institute of Computer Science, University Leipzig, Leipzig, Germany
| | - Martin Middendorf
- Swarm Intelligence and Complex Systems Group, Institute of Computer Science, University Leipzig, Leipzig, Germany.
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Lee Y, Morrow EM. Quantitative Measurement of Tau Aggregation in Genetically Modified Rats with Neurodegeneration. Methods Mol Biol 2024; 2761:291-299. [PMID: 38427245 DOI: 10.1007/978-1-0716-3662-6_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Animal models of neurodegenerative diseases have helped us to better understand the pathogenesis of neurodegenerative diseases. However, recent failure to translate pre-clinical model studies to the clinic urges us to develop more rigorous and faithful animal models in neurodegenerative diseases. As genetic manipulation of rats becomes much more accessible due to availability of CRISPR-Cas9 and other genomic editing toolboxes, rats have been emerging as a new model system for neurodegenerative diseases. Even though mouse models have been dominant over the last decades, rats may provide advantages over mice. Rats are more genetically and physiologically closer to humans than to mice. Also, certain rat models can represent deposition of tau, which is one of the key pathological features of Alzheimer's diseases and tauopathies. However, there is an unmet need for standardized, rigorous testing in rat models. We adopted two commonly used biochemical and immunofluorescence methods from mice and human postmortem brains to measure tau aggregation. Due to the intrinsic differences between mice and rats, e.g., size of rat brains, certain equipment is required for rat models to study tau pathologies. Along with specific tools, here we describe the detailed methods for rat models of neurodegenerative diseases.
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Affiliation(s)
- YouJin Lee
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.
- Center for Translational Neuroscience, Carney Institute for Brain Science, and Brown Institute for Translational Science (BITS), Brown University, Providence, RI, USA.
| | - Eric M Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.
- Center for Translational Neuroscience, Carney Institute for Brain Science, and Brown Institute for Translational Science (BITS), Brown University, Providence, RI, USA.
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Zhao YJ, Zhou C, Wei YY, Zhang SY, Mishra JS, Li HH, Lei W, Wang K, Kumar S, Zheng J. An Endogenous Aryl Hydrocarbon Receptor Ligand Induces Preeclampsia-like Phenotypes: Transcriptome, Phosphoproteome, and Cell Functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572271. [PMID: 38187714 PMCID: PMC10769228 DOI: 10.1101/2023.12.20.572271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Background Preeclampsia (PE) is one hypertensive disorder and a leading cause of maternal and fetal mortality and morbidity during human pregnancy. Aryl hydrocarbon receptor (AhR) is a transcription factor, which regulates vascular functions. Exogenous and endogenous AhR ligands can induce hypertension in animals. However, if dysregulation of endogenous AhR ligands contributes to the pathophysiology of PE remains elusive. Methods We measured AhR activities in human maternal and umbilical vein sera. We also applied physiological, cellular, and molecular approaches to dissect the role of endogenous AhR ligands in vascular functions during pregnancy using pregnant rats and primary human umbilical vein endothelial cells (HUVECs) as models. Results PE elevated AhR activities in human umbilical vein sera. Exposure of pregnant rats to an endogenous AhR ligand, 2-(1'H-indole-3'-carbonyl)-thiazole-4-carboxylic acid methyl ester (ITE) increased blood pressure and proteinuria, while decreased uteroplacental blood flow and reduced fetal and placental weights, all of which are hallmarks of PE. ITE dampened vascular growth and fetal sex-specifically altered immune cell infiltration in rat placentas. ITE also decreased cell proliferation and cell monolayer integrity in HUVECs in vitro . RNA sequencing analysis revealed that ITE dysregulated transcriptome in rat placentas and HUVECs in a fetal sex-specific manner. Bottom-up phosphoproteomics showed that ITE disrupted phosphoproteome in HUVECs. These ITE-dysregulated genes and phosphoproteins were enriched in biological functions and pathways which are highly relevant to diseases of heart, liver, and kidney, vascular functions, inflammation responses, cell death, and kinase inhibition. Conclusions Dysregulation of endogenous AhR ligands during pregnancy may lead to the development of PE with underlying impaired vascular functions, fetal sex-specific immune cell infiltration and transcriptome, and phosphoproteome. Thus, this study has provided a novel mechanism for the development of PE and potentially other forms of hypertensive pregnancies. These AhR ligand-activated genes and phosphoproteins might represent promising therapeutic and fetal sex-specific targets for PE-impaired vascular functions.
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Park KC, Crump NT, Louwman N, Krywawych S, Cheong YJ, Vendrell I, Gill EK, Gunadasa-Rohling M, Ford KL, Hauton D, Fournier M, Pires E, Watson L, Roseman G, Holder J, Koschinski A, Carnicer R, Curtis MK, Zaccolo M, Hulikova A, Fischer R, Kramer HB, McCullagh JSO, Trefely S, Milne TA, Swietach P. Disrupted propionate metabolism evokes transcriptional changes in the heart by increasing histone acetylation and propionylation. NATURE CARDIOVASCULAR RESEARCH 2023; 2:1221-1245. [PMID: 38500966 PMCID: PMC7615744 DOI: 10.1038/s44161-023-00365-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/15/2023] [Indexed: 03/20/2024]
Abstract
Propiogenic substrates and gut bacteria produce propionate, a post-translational protein modifier. In this study, we used a mouse model of propionic acidaemia (PA) to study how disturbances to propionate metabolism result in histone modifications and changes to gene expression that affect cardiac function. Plasma propionate surrogates were raised in PA mice, but female hearts manifested more profound changes in acyl-CoAs, histone propionylation and acetylation, and transcription. These resulted in moderate diastolic dysfunction with raised diastolic Ca2+, expanded end-systolic ventricular volume and reduced stroke volume. Propionate was traced to histone H3 propionylation and caused increased acetylation genome-wide, including at promoters of Pde9a and Mme, genes related to contractile dysfunction through downscaled cGMP signaling. The less severe phenotype in male hearts correlated with β-alanine buildup. Raising β-alanine in cultured myocytes treated with propionate reduced propionyl-CoA levels, indicating a mechanistic relationship. Thus, we linked perturbed propionate metabolism to epigenetic changes that impact cardiac function.
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Affiliation(s)
- Kyung Chan Park
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Nicholas T. Crump
- MRC Molecular Haematology Unit, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Present Address: Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Niamh Louwman
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Steve Krywawych
- Department of Chemical Pathology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Yuen Jian Cheong
- Epigenetics & Signalling Programmes, Babraham Institute, Cambridge, UK
| | - Iolanda Vendrell
- Nuffield Department of Medicine, Target Discovery Institute, Oxford, UK
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Eleanor K. Gill
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | | | - Kerrie L. Ford
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - David Hauton
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | | | - Lydia Watson
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Gerald Roseman
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - James Holder
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Andreas Koschinski
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Ricardo Carnicer
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - M. Kate Curtis
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Manuela Zaccolo
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Alzbeta Hulikova
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, Oxford, UK
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Holger B. Kramer
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Sophie Trefely
- Epigenetics & Signalling Programmes, Babraham Institute, Cambridge, UK
| | - Thomas A. Milne
- MRC Molecular Haematology Unit, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Pawel Swietach
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
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Seki S, Kawabe T, Yamazaki W, Matsumura K, Oikawa T, Obata T, Higashiya M, Yano M, Eto T. Cryopreservation of rat embryos at all developmental stages by small-volume vitrification procedure and rapid warming in cryotubes. Sci Rep 2023; 13:20903. [PMID: 38017006 PMCID: PMC10684866 DOI: 10.1038/s41598-023-47394-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023] Open
Abstract
Intracellular ice formation during cryopreservation is lethal to the cell, including during warming. Here, we examined the effect of sample volume and warming rate on the cryopreservation success of 1-cell rat embryos based on successful development into blastocysts in vitro and to term in vivo following embryo transfer. Embryos were equilibrated in 5% propylene glycol solution for 10 min, held for 40 s at 0 °C in cryopreservation solution (5%PG + PEPeS), and cooled by immersion in liquid nitrogen. When 1-cell embryos were cryopreserved in a volume of 30-100 μL at a cooling rate of 5830-7160 °C/min and warmed at 35,480-49,400 °C/min by adding 1 mL of 0.3 M sucrose solution at 50 °C, 17.3-28.8% developed into blastocysts, compared with 57.0% of untreated embryos. However, when 1-cell embryos were cryopreserved in a smaller volume of 15 μl at 7950 °C/min and warmed at 68,850 °C/min, 58.8 ± 10.6% developed into blastocysts and 50.0 ± 7.4% developed to term, comparable to that of non-treated embryos (57.0 ± 5.4% and 51.4 ± 3.1%, respectively). Cryopreserved embryos at other developmental stages also showed high in vitro culture potential similar to that of the control. Using a conventional cryotube and a small-volume vitrification procedure with rapid warming, we achieved high levels of subsequent rat embryonic development at all developmental stages.
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Affiliation(s)
- Shinsuke Seki
- Experimental Animal Division, Bioscience Education and Research Support Center, Akita University, 1-1-1 Hondo, Akita, Akita, 010-8543, Japan.
| | - Toshiaki Kawabe
- ARK Resource Co., Ltd., 456 Osozu, Misato-machi, Shimomashiki-gun, Kumamoto, 861-4401, Japan
| | - Wataru Yamazaki
- Experimental Animal Division, Bioscience Education and Research Support Center, Akita University, 1-1-1 Hondo, Akita, Akita, 010-8543, Japan
| | - Kazuaki Matsumura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa, 923-1292, Japan
| | - Takanori Oikawa
- Experimental Animal Division, Bioscience Education and Research Support Center, Akita University, 1-1-1 Hondo, Akita, Akita, 010-8543, Japan
| | - Takahiro Obata
- Experimental Animal Division, Bioscience Education and Research Support Center, Akita University, 1-1-1 Hondo, Akita, Akita, 010-8543, Japan
| | - Misako Higashiya
- Experimental Animal Division, Bioscience Education and Research Support Center, Akita University, 1-1-1 Hondo, Akita, Akita, 010-8543, Japan
| | - Megumi Yano
- Experimental Animal Division, Bioscience Education and Research Support Center, Akita University, 1-1-1 Hondo, Akita, Akita, 010-8543, Japan
| | - Tomoo Eto
- Central Institute for Experimental Animals, 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan.
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Zhang L, Huang J, Dai L, Zhu G, Yang XL, He Z, Li YH, Yang H, Zhang CQ, Shen KF, Liang P. Expression profiles of α-synuclein in cortical lesions of patients with FCD IIb and TSC, and FCD rats. Front Neurol 2023; 14:1255097. [PMID: 38020594 PMCID: PMC10662349 DOI: 10.3389/fneur.2023.1255097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Background Focal cortical dysplasia (FCD) IIb and tuberous sclerosis complex (TSC) are common causes of drug-resistant epilepsy in children. However, the etiologies related to the development of FCD IIb and TSC are not fully understood. α-synuclein (α-syn) is a member of synucleins family that plays crucial roles in modulating synaptic transmission in central nervous system. Here, we explored the expression profiles and potential pathogenic functions of α-syn in cortical lesions of epileptic patients with FCD IIb and TSC. Methods Surgical specimens from epileptic patients with FCD IIb and TSC, as well as FCD rats generated by in utero X-ray-radiation were adopted in this study and studied with immunohistochemistry, immunofluorescence, western blotting, and co-immunoprecipitation etc. molecular biological techniques. Result Our results showed that α-syn expression was reduced in FCD IIb and TSC lesions. Specifically, α-syn protein was intensely expressed in dysplastic neurons (DNs) and balloon cells (BCs) in FCD IIb lesions, whereas was barely detected in DNs and giant cells (GCs) of TSC lesions. Additionally, p-α-syn, the aggregated form of α-syn, was detected in DNs, BCs, GCs, and glia-like cells of FCD IIb and TSC lesions. We previous showed that the function of N-methyl-D-aspartate receptor (NMDAR) was enhanced in FCD rats generated by X-ray-radiation. Here, we found the interaction between α-syn and NMDAR subunits NMDAR2A, NMDAR2B were augmented in cortical lesions of FCD patients and FCD rats. Conclusion These results suggested a potential role of α-syn in the pathogenesis of FCD IIb and TSC by interfering with NMDAR.
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Affiliation(s)
- Li Zhang
- Department of Neurosurgery, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Jun Huang
- Department of Neurosurgery, Epilepsy Research Center of PLA, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Lu Dai
- Chongqing Institute for Brain and Intelligence, Guang Yang Bay Laboratory, Chongqing, China
| | - Gang Zhu
- Department of Neurosurgery, Epilepsy Research Center of PLA, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xiao-Lin Yang
- Department of Neurosurgery, Epilepsy Research Center of PLA, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Zeng He
- Department of Neurosurgery, Epilepsy Research Center of PLA, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yu-Hong Li
- Department of Cell Biology, Basic Medical College, Army Medical University, Chongqing, China
| | - Hui Yang
- Department of Neurosurgery, Epilepsy Research Center of PLA, Xinqiao Hospital, Army Medical University, Chongqing, China
- Chongqing Institute for Brain and Intelligence, Guang Yang Bay Laboratory, Chongqing, China
| | - Chun-Qing Zhang
- Department of Neurosurgery, Epilepsy Research Center of PLA, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Kai-Feng Shen
- Department of Neurosurgery, Epilepsy Research Center of PLA, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Ping Liang
- Department of Neurosurgery, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
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Shah T, Hou Y, Jiang J, Shah Z, Wang Y, Li Q, Xu X, Wang Y, Wang B, Xia X. Comparative analysis of the intestinal microbiome in Rattus norvegicus from different geographies. Front Microbiol 2023; 14:1283453. [PMID: 38029126 PMCID: PMC10655115 DOI: 10.3389/fmicb.2023.1283453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Rat species Rattus norvegicus, also known as the brown street rat, is the most abundant mammal after humans in urban areas, where they co-exist with humans and domestic animals. The reservoir role of R. norvegicus of zoonotic pathogens in cities among rodent-borne diseases that could endanger the lives of humans and other mammals. Therefore, understanding the normal microbiome of R. norvegicus is crucial for understanding and preventing zoonotic pathogen transmission to humans and animals. We investigated the intestinal microbiome of free-living R. norvegicus collected from the Ruili, Nujiang, and Lianhe regions of Yunnan, China, using 16S rRNA gene sequence analysis. Proteobacteria, followed by Firmicutes, and Bacteroidetes were abundant in the intestines of R. norvegicus; however, bacterial compositions varied significantly between samples from different locations. Following a similar trend, Gammaproteobacteria, Bacilli, and Clostridia were among the top bacterial classes in most intestinal samples. The situation differed slightly for the Lianhe and Nujiang samples, although Phyla Bacteroidota and Spirochaetota were most prevalent. The Alpha diversity, Chao1, and Simpson indexes revealed microbial richness among the R. norvegicus samples. A slight variation was observed among the samples collected from Ruili, Nujiang, and Lianhe. At species levels, several opportunistic and zoonotic bacterial pathogens, including Lactococcus garvieae, Uruburuella suis, Bartonella australis, Clostridium perfringens, Streptococcus azizii, Vibrio vulnificus, etc., were revealed in the R. norvegicus intestines, implying the need for a regular survey to monitor and control rodent populations. In conclusion, we explored diverse microbial communities in R. norvegicus intestines captured from different regions. Further, we identified several opportunistic and potential bacterial pathogens, which still need to be tested for their underlying pathogenesis. The findings of our current study should be considered a warning to the health authorities to implement rat control and surveillance strategies globally.
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Affiliation(s)
- Taif Shah
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Jinyong Jiang
- Yunnan International Joint Laboratory of Vector Biology and Control & Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research of Yunnan Institute of Parasitic Diseases, Yunnan, China
| | - Zahir Shah
- College of Veterinary Sciences, The University of Agriculture, Peshawar, Pakistan
| | - Yuhan Wang
- Research Institute of Forest Protection, Yunnan Academy of Forestry and Grassland, Kunming, Yunnan, China
| | - Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Xiang Xu
- Yunnan International Joint Laboratory of Vector Biology and Control & Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research of Yunnan Institute of Parasitic Diseases, Yunnan, China
| | - Yixuan Wang
- Research Institute of Forest Protection, Yunnan Academy of Forestry and Grassland, Kunming, Yunnan, China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- School of Public Health, Kunming Medical University, Kunming, Yunnan, China
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Yuan X, Yan F, Gao L, Ma Q, Wang J. Hypericin as a potential drug for treating Alzheimer's disease and type 2 diabetes with a view to drug repositioning. CNS Neurosci Ther 2023; 29:3307-3321. [PMID: 37183545 PMCID: PMC10580347 DOI: 10.1111/cns.14260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/25/2023] [Accepted: 04/29/2023] [Indexed: 05/16/2023] Open
Abstract
AIMS Alzheimer's disease (AD) and type 2 diabetes (T2D) are two of the most common diseases in elderly population and they have a high rate of comorbidity. Study has revealed that T2D is a major risk factor of AD, and thus exploring therapeutic approaches that can target both diseases has drawn much interest in recent years. In this study, we tried to explore drugs that could be potentially used to prevent or treat both AD and T2D via a drug repositioning approach. METHODS We first searched the known drugs that may be effective to T2D treatment based on the network distance between the T2D-associated genes and drugs deposited in the DrugBank database. Then, via molecular docking, we further screened these drugs by examining their interaction with islet amyloid polypeptide (IAPP) and Aβ42 peptide, the key components involved in the pathogenesis of T2D or AD. Finally, the binding between the selected drug candidates and the target proteins was verified by molecular dynamics (MD) simulation; and the potential function of the drug candidates and the corresponding targets were analyzed. RESULTS From multiple resources, 734 T2D-associated genes were collected, and a list of 1109 drug candidates for T2D was obtained. We found that hypericin had the lowest binding energy and the most stable interaction with either IAPP or Aβ42 peptide. In addition, we also found that the target genes regulated by hypericin were differentially expressed in the tissues related to the two diseases. CONCLUSION Our results show that hypericin may be able to bind with IAPP and Aβ42 stably and prevent their accumulation, and thus could be a promising drug candidate for treating the comorbidity of AD and T2D.
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Affiliation(s)
- Xin Yuan
- School of Biomedical EngineeringTianjin Medical UniversityTianjinChina
| | - Fei Yan
- School of Biomedical EngineeringTianjin Medical UniversityTianjinChina
| | - Li‐Hui Gao
- School of Biomedical EngineeringTianjin Medical UniversityTianjinChina
| | - Qian‐Hui Ma
- School of Biomedical EngineeringTianjin Medical UniversityTianjinChina
| | - Ju Wang
- School of Biomedical EngineeringTianjin Medical UniversityTianjinChina
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Udagawa H, Funahashi N, Nishimura W, Uebanso T, Kawaguchi M, Asahi R, Nakajima S, Nammo T, Hiramoto M, Yasuda K. Glucocorticoid receptor-NECAB1 axis can negatively regulate insulin secretion in pancreatic β-cells. Sci Rep 2023; 13:17958. [PMID: 37863964 PMCID: PMC10589354 DOI: 10.1038/s41598-023-44324-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023] Open
Abstract
The mechanisms of impaired glucose-induced insulin secretion from the pancreatic β-cells in obesity have not yet been completely elucidated. Here, we aimed to assess the effects of adipocyte-derived factors on the functioning of pancreatic β-cells. We prepared a conditioned medium using 3T3-L1 cell culture supernatant collected at day eight (D8CM) and then exposed the rat pancreatic β-cell line, INS-1D. We found that D8CM suppressed insulin secretion in INS-1D cells due to reduced intracellular calcium levels. This was mediated by the induction of a negative regulator of insulin secretion-NECAB1. LC-MS/MS analysis results revealed that D8CM possessed steroid hormones (cortisol, corticosterone, and cortisone). INS-1D cell exposure to cortisol or corticosterone increased Necab1 mRNA expression and significantly reduced insulin secretion. The increased expression of Necab1 and reduced insulin secretion effects from exposure to these hormones were completely abolished by inhibition of the glucocorticoid receptor (GR). NECAB1 expression was also increased in the pancreatic islets of db/db mice. We demonstrated that the upregulation of NECAB1 was dependent on GR activation, and that binding of the GR to the upstream regions of Necab1 was essential for this effect. NECAB1 may play a novel role in the adipoinsular axis and could be potentially involved in the pathophysiology of obesity-related diabetes mellitus.
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Affiliation(s)
- Haruhide Udagawa
- Department of Metabolic Disorder, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, 162-8655, Japan
- Department of Registered Dietitians, Faculty of Health and Nutrition, Bunkyo University, 1100 Namegaya, Chigasaki, Kanagawa, 253-8550, Japan
| | - Nobuaki Funahashi
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Wataru Nishimura
- Department of Molecular Biology, International University of Health and Welfare School of Medicine, Narita, Chiba, 286-8686, Japan
- Division of Anatomy, Bio-Imaging and Neuro-Cell Science, Jichi Medical University, Shimotsuke, Tochigi, 329-0498, Japan
| | - Takashi Uebanso
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan
| | - Miho Kawaguchi
- Department of Metabolic Disorder, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Riku Asahi
- Department of Registered Dietitians, Faculty of Health and Nutrition, Bunkyo University, 1100 Namegaya, Chigasaki, Kanagawa, 253-8550, Japan
| | - Shigeru Nakajima
- Department of Registered Dietitians, Faculty of Health and Nutrition, Bunkyo University, 1100 Namegaya, Chigasaki, Kanagawa, 253-8550, Japan
| | - Takao Nammo
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Diabetes Care Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Masaki Hiramoto
- Department of Biochemistry, Tokyo Medical University, Tokyo, 160-8402, Japan
| | - Kazuki Yasuda
- Department of Metabolic Disorder, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, 162-8655, Japan.
- Department of Diabetes, Endocrinology and Metabolism, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo, 181-8611, Japan.
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Kopania EEK, Thomas GWC, Hutter CR, Mortimer SME, Callahan CM, Roycroft E, Achmadi AS, Breed WG, Clark NL, Esselstyn JA, Rowe KC, Good JM. Molecular evolution of male reproduction across species with highly divergent sperm morphology in diverse murine rodents. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555585. [PMID: 37693452 PMCID: PMC10491253 DOI: 10.1101/2023.08.30.555585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Sperm competition can drive rapid evolution of male reproductive traits, but it remains unclear how variation in sperm competition intensity shapes phenotypic and molecular diversity across clades. Old World mice and rats (subfamily Murinae) comprise a rapid radiation and exhibit incredible diversity in sperm morphology and production. We combined phenotype and sequence data to model the evolution of reproductive traits and genes across 78 murine species. We identified several shifts towards smaller relative testes mass, a trait reflective of reduced sperm competition. Several sperm traits were associated with relative testes mass, suggesting that mating system evolution likely selects for convergent traits related to sperm competitive ability. Molecular evolutionary rates of spermatogenesis proteins also correlated with relative testes mass, but in an unexpected direction. We predicted that sperm competition would result in rapid divergence among species with large relative testes mass, but instead found that many spermatogenesis genes evolve more rapidly in species with smaller relative testes mass due to relaxed purifying selection. While some reproductive genes evolved under positive selection, relaxed selection played a greater role underlying rapid evolution in small testes species. Our work demonstrates that sexual selection can impose strong purifying selection shaping the evolution of male reproduction.
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Thomas GWC, Hughes JJ, Kumon T, Berv JS, Nordgren CE, Lampson M, Levine M, Searle JB, Good JM. The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555178. [PMID: 37693498 PMCID: PMC10491188 DOI: 10.1101/2023.08.28.555178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.
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Affiliation(s)
- Gregg W. C. Thomas
- Division of Biological Sciences, University of Montana, Missoula, MT, 59801
- Informatics Group, Harvard University, Cambridge, MA, 02138
| | - Jonathan J. Hughes
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, 92521
| | - Tomohiro Kumon
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Jacob S. Berv
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109
| | - C. Erik Nordgren
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Michael Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Mia Levine
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, MT, 59801
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TERZİ Ü, ATEŞ İ. SJÖGREN SENDROMU İLE BAZI GEN POLİMORFİZMLERİ ARASINDAKİ OLASI BAĞLANTILAR. ANKARA UNIVERSITESI ECZACILIK FAKULTESI DERGISI 2023; 47:7-7. [DOI: 10.33483/jfpau.1328811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
Objective: Sjögren’s syndrome is a complex and widespread autoimmune disease whose pathogenesis is not fully elucidated and environmental and genetic factors affect the development of the disease. In order to reveal the effect of genetic contribution, studies have been conducted on the genes previously shown to play a role in other autoimmune diseases such as systemic lupus erythromatosus. In addition, two GWAS studies were conducted to investigate the role of more genes in the disease by screening the entire genome and the relationship of previously unknown genes with SS was shown.
Result and Discussion: Studies are being conducted with spontaneous and genetically modified animal models in order to better reveal the relationship between SS and genes and to reinforce the data obtained from humans. In this study, the relationship between the genes previously studied in other autoimmune diseases and the genes associated with SS in GWAS studies and the possible pathways that may contribute to the pathogenesis of the disease through related genes were investigated.
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Affiliation(s)
- Ülkü TERZİ
- ANKARA ÜNİVERSİTESİ, ECZACILIK FAKÜLTESİ, ECZACILIK MESLEK BİLİMLERİ BÖLÜMÜ, FARMASOTİK TOKSİKOLOJİ ANABİLİM DALI
| | - İlker ATEŞ
- ANKARA ÜNİVERSİTESİ, ECZACILIK FAKÜLTESİ, ECZACILIK MESLEK BİLİMLERİ BÖLÜMÜ, FARMASOTİK TOKSİKOLOJİ ANABİLİM DALI
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36
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Neamtu A, Serban DN, Barritt GJ, Isac DL, Vasiliu T, Laaksonen A, Serban IL. Molecular dynamics simulations reveal the hidden EF-hand of EF-SAM as a possible key thermal sensor for STIM1 activation by temperature. J Biol Chem 2023; 299:104970. [PMID: 37380078 PMCID: PMC10400917 DOI: 10.1016/j.jbc.2023.104970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/07/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
Intracellular calcium signaling is essential for many cellular processes, including store-operated Ca2+ entry (SOCE), which is initiated by stromal interaction molecule 1 (STIM1) detecting endoplasmic reticulum (ER) Ca2+ depletion. STIM1 is also activated by temperature independent of ER Ca2+ depletion. Here we provide evidence, from advanced molecular dynamics simulations, that EF-SAM may act as a true temperature sensor for STIM1, with the prompt and extended unfolding of the hidden EF-hand subdomain (hEF) even at slightly elevated temperatures, exposing a highly conserved hydrophobic Phe108. Our study also suggests an interplay between Ca2+ and temperature sensing, as both, the canonical EF-hand subdomain (cEF) and the hidden EF-hand subdomain (hEF), exhibit much higher thermal stability in the Ca2+-loaded form compared to the Ca2+-free form. The SAM domain, surprisingly, displays high thermal stability compared to the EF-hands and may act as a stabilizer for the latter. We propose a modular architecture for the EF-hand-SAM domain of STIM1 composed of a thermal sensor (hEF), a Ca2+ sensor (cEF), and a stabilizing domain (SAM). Our findings provide important insights into the mechanism of temperature-dependent regulation of STIM1, which has broad implications for understanding the role of temperature in cellular physiology.
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Affiliation(s)
- Andrei Neamtu
- Department of Physiology, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Romania; Center of Advanced Research in Bionanocojugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry Iasi, Iasi, Romania
| | - Dragomir N Serban
- Department of Physiology, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Romania.
| | - Greg J Barritt
- Discipline of Medical Biochemistry, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Dragos Lucian Isac
- Center of Advanced Research in Bionanocojugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry Iasi, Iasi, Romania
| | - Tudor Vasiliu
- Center of Advanced Research in Bionanocojugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry Iasi, Iasi, Romania
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden; Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, Romania; State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, P. R. China
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37
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Shegarfi H. Recognition of Listeria monocytogenes infection by natural killer cells: Towards a complete picture by experimental studies in rats. Innate Immun 2023; 29:110-121. [PMID: 37285590 PMCID: PMC10468624 DOI: 10.1177/17534259231178223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 04/11/2023] [Accepted: 05/08/2023] [Indexed: 06/09/2023] Open
Abstract
The study of cellular immune responses in animal disease models demands detailed knowledge of development, function, and regulation of immune cells, including natural killer (NK) cells. Listeria monocytogenes (LM) bacterium has been explored in a large area of research fields, including the host pathogen interaction. Although the importance role of NK cells in controlling the first phase of LM burden has been investigated, the interaction between NK cells and infected cells in details are far from being comprehended. From in vivo and in vitro experiments, we can drive several important pieces of knowledge that hopefully contribute to illuminating the intercommunication between LM-infected cells and NK cells. Experimental studies performed in rats revealed that certain NK cell ligands are influenced in LM-infected cells. These ligands include both classical- and non-classical MHC class I molecules and C-type lectin related (Clr) molecules that are ligands for Ly49- and NKR-P1 receptors respectively. Interaction between these receptors:ligands during LM infection, demonstrated stimulation of rat NK cells. Hence, these studies provided additional knowledge to the mechanisms NK cells utilise to recognise and respond to LM infection outlined in the current review.
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38
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Luzuriaga-Neira AR, Ritchie AM, Payne BL, Carrillo-Parramon O, Liberles DA, Alvarez-Ponce D. Highly Abundant Proteins Are Highly Thermostable. Genome Biol Evol 2023; 15:evad112. [PMID: 37399326 DOI: 10.1093/gbe/evad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2023] [Indexed: 07/05/2023] Open
Abstract
Highly abundant proteins tend to evolve slowly (a trend called E-R anticorrelation), and a number of hypotheses have been proposed to explain this phenomenon. The misfolding avoidance hypothesis attributes the E-R anticorrelation to the abundance-dependent toxic effects of protein misfolding. To avoid these toxic effects, protein sequences (particularly those of highly expressed proteins) would be under selection to fold properly. One prediction of the misfolding avoidance hypothesis is that highly abundant proteins should exhibit high thermostability (i.e., a highly negative free energy of folding, ΔG). Thus far, only a handful of analyses have tested for a relationship between protein abundance and thermostability, producing contradictory results. These analyses have been limited by 1) the scarcity of ΔG data, 2) the fact that these data have been obtained by different laboratories and under different experimental conditions, 3) the problems associated with using proteins' melting energy (Tm) as a proxy for ΔG, and 4) the difficulty of controlling for potentially confounding variables. Here, we use computational methods to compare the free energy of folding of pairs of human-mouse orthologous proteins with different expression levels. Even though the effect size is limited, the most highly expressed ortholog is often the one with a more negative ΔG of folding, indicating that highly expressed proteins are often more thermostable.
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Affiliation(s)
| | - Andrew M Ritchie
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, USA
| | | | | | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, USA
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39
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Liu Y, Ge D, Zhou J, Chu Y, Zheng X, Ke L, Li P, Lu Y, Zou X, Xia L, Liu Y, Huang C, Shen C, Chu Y. HS-SPME-GC-MS Untargeted Analysis of Normal Rat Organs Ex Vivo: Differential VOC Discrimination and Fingerprint VOC Identification. Anal Chem 2023. [PMID: 37392185 DOI: 10.1021/acs.analchem.3c01546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2023]
Abstract
The investigation of volatile organic compounds (VOCs) in human metabolites has been a topic of interest as it holds the potential for the development of non-invasive technologies to screen for organ lesions in vivo. However, it remains unclear whether VOCs differ among healthy organs. Consequently, a study was conducted to analyze VOCs in ex vivo organ tissues obtained from 16 Wistar rats, comprising 12 different organs. The VOCs released from each organ tissue were detected by the headspace-solid phase microextraction-gas chromatography-mass spectrometry technique. In the untargeted analysis of 147 chromatographic peaks, the differential volatiles of rat organs were explored based on the Mann-Whitney U test and fold change (FC > 2.0) compared with other organs. It was found that there were differential VOCs in seven organs. A discussion on the possible metabolic pathways and related biomarkers of organ differential VOCs was conducted. Based on the orthogonal partial least squares discriminant analysis and receiver operating characteristic curve, we found that differential VOCs in the liver, cecum, spleen, and kidney can be used as the unique identification of the corresponding organ. In this study, differential VOCs of organs in rats were systematically reported for the first time. Profiles of VOCs produced by healthy organs can serve as a reference or baseline that may indicate the presence of disease or abnormalities in the organ's function. Differential VOCs can be used as the fingerprint of organs, and future integration with metabolic research may contribute to the development of healthcare.
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Affiliation(s)
- Yue Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
- University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Dianlong Ge
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
| | - Jijuan Zhou
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
- University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Yajing Chu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
- University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Xiangxue Zheng
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, Anhui, China
| | - Li Ke
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
- University of Science and Technology of China, Hefei 230026, Anhui, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, P. R. China
| | - Pan Li
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
| | - Yan Lu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui, China
| | - Xue Zou
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
| | - Lei Xia
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
| | - Yawei Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
| | - Chaoqun Huang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
| | - Chengyin Shen
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui, China
| | - Yannan Chu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
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40
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Gable SM, Mendez JM, Bushroe NA, Wilson A, Byars MI, Tollis M. The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order. Genes (Basel) 2023; 14:1387. [PMID: 37510292 PMCID: PMC10379679 DOI: 10.3390/genes14071387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of genomic investigations into the patterns and processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, and evolutionary analysis. We survey the most recently available whole genome assemblies for squamates, including the taxonomic distribution of available squamate genomes, and assess their quality metrics and usefulness for research. We then focus on disagreements in squamate phylogenetic inference, how methods of high-throughput phylogenomics affect these inferences, and demonstrate the promise of whole genomes to settle or sustain persistent phylogenetic arguments for squamates. We review the role transposable elements play in vertebrate evolution, methods of transposable element annotation and analysis, and further demonstrate that through the understanding of the diversity, abundance, and activity of transposable elements in squamate genomes, squamates can be an ideal model for the evolution of genome size and structure in vertebrates. We discuss how squamate genomes can contribute to other areas of biological research such as venom systems, studies of phenotypic evolution, and sex determination. Because they represent more than 30% of the living species of amniote, squamates deserve a genome consortium on par with recent efforts for other amniotes (i.e., mammals and birds) that aim to sequence most of the extant families in a clade.
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Affiliation(s)
- Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jasmine M Mendez
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Nicholas A Bushroe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Adam Wilson
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Michael I Byars
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
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41
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Ricci M, Peona V, Boattini A, Taccioli C. Comparative analysis of bats and rodents' genomes suggests a relation between non-LTR retrotransposons, cancer incidence, and ageing. Sci Rep 2023; 13:9039. [PMID: 37270634 DOI: 10.1038/s41598-023-36006-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/27/2023] [Indexed: 06/05/2023] Open
Abstract
The presence in nature of species showing drastic differences in lifespan and cancer incidence has recently increased the interest of the scientific community. In particular, the adaptations and the genomic features underlying the evolution of cancer-resistant and long-lived organisms have recently focused on transposable elements (TEs). In this study, we compared the content and dynamics of TE activity in the genomes of four rodent and six bat species exhibiting different lifespans and cancer susceptibility. Mouse, rat, and guinea pig genomes (short-lived and cancer-prone organisms) were compared with that of naked mole rat (Heterocephalus glaber) which is a cancer-resistant organism and the rodent with the longest lifespan. The long-lived bats of the genera Myotis, Rhinolophus, Pteropus and Rousettus were instead compared with Molossus molossus, which is one of the organisms with the shortest lifespan among the order Chiroptera. Despite previous hypotheses stating a substantial tolerance of TEs in bats, we found that long-lived bats and the naked mole rat share a marked decrease of non-LTR retrotransposons (LINEs and SINEs) accumulation in recent evolutionary times.
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Affiliation(s)
| | - Valentina Peona
- Department of Organismal Biology, Systematic Biology, Uppsala University, Uppsala, Sweden.
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Cristian Taccioli
- Department of Animal Medicine, Health and Production, University of Padova, Padua, Italy
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42
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Session AM, Rokhsar DS. Transposon signatures of allopolyploid genome evolution. Nat Commun 2023; 14:3180. [PMID: 37263993 DOI: 10.1038/s41467-023-38560-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/08/2023] [Indexed: 06/03/2023] Open
Abstract
Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus, and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids.
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Affiliation(s)
- Adam M Session
- Department of Molecular and Cell, University of California, Berkeley, CA, 94720, USA.
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Department of Biological Sciences, Binghamton University, Binghamton, NY, 13902, USA.
| | - Daniel S Rokhsar
- Department of Molecular and Cell, University of California, Berkeley, CA, 94720, USA
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Molecular Genetics Unit, Okinawa Institute for Science and Technology Graduate University, Okinawa, Japan
- Chan Zuckerberg BioHub, San Francisco, CA, USA
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43
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Li Z, Wang Q, Lv N, Xu G, Yang X, Zhu B. Genome-wide identification of endogenous retrovirus elements and their active transcription in mink genome. MLIFE 2023; 2:201-208. [PMID: 38817617 PMCID: PMC10989824 DOI: 10.1002/mlf2.12074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/12/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2024]
Abstract
Mammalian endogenous retroviruses (ERVs) are ancient retroviruses that have been integrated into genomes. ERVs were believed to be inactive until the discovery of ERV transcription in the mouse genome. However, the transcription level and function of ERV elements in mammalian genomes are not well understood. In this study, we performed the first genome-wide scanning of ERV loci in the American mink (Neogale vison) genome (NeoERV) followed by transcriptomic analysis to detect actively transcribed NeoERV elements. A total of 365,791 NeoERV loci were identified, and161,205 (44%) of these loci were found to be actively transcribed based on transcriptomic data from three types of tissues (amygdala, trachea and lung). More than one third of the actively transcribed NeoERV loci were tissue-specific. Furthermore, some of the active loci were associated with host gene transcription, and the level of NeoERV transcription was positively correlated with that of host genes, specifically when active loci were located in overlapped gene regions. An in-depth analysis of the envelope protein coding env gene showed that, in general, its transcription level was higher than that of NeoERVs, which is believed to be associated with host immunity.
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Affiliation(s)
- Zheng Li
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qing Wang
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- Jiangxi Science and Technology Normal UniversityNanchangChina
| | - Na Lv
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- Jinan Microecological Biomedicine Shandong LaboratoryJinanChina
| | - Guojin Xu
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Xuemei Yang
- Beijing Pediatric Research InstituteBeijingChina
| | - Baoli Zhu
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Jinan Microecological Biomedicine Shandong LaboratoryJinanChina
- Department of Pathogenic Biology, School of Basic Medical SciencesSouthwest Medical UniversityLuzhouChina
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44
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Sathiaseelan R, Ahn B, Stout M, Logan S, Wanagat J, Nguyen H, Hord N, Vandiver A, Selvarani R, Ranjit R, Yarbrough H, Masingale A, Miller B, Wolf R, Austad S, Richardson A. A Genetically Heterogeneous Rat Model with Divergent Mitochondrial Genomes. J Gerontol A Biol Sci Med Sci 2023; 78:771-779. [PMID: 36762848 PMCID: PMC10172978 DOI: 10.1093/gerona/glad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Indexed: 02/11/2023] Open
Abstract
We generated a genetically heterogenous rat model by a 4-way cross strategy using 4 inbred strains (Brown Norway [BN], Fischer 344 [F344], Lewis [LEW], and Wistar Kyoto [KY]) to provide investigators with a highly genetically diverse rat model from commercially available inbred rats. We made reciprocal crosses between males and females from the 2 F1 hybrids to generate genetically heterogeneous rats with mitochondrial genomes from either the BN (OKC-HETB, a.k.a "B" genotype) or WKY (OKC-HETW a.k.a "W" genotype) parental strains. These two mitochondrial genomes differ at 94 nucleotides, more akin to human mitochondrial genome diversity than that available in classical laboratory mouse strains. Body weights of the B and W genotypes were similar. However, mitochondrial genotype antagonistically affected grip strength and treadmill endurance in females only. In addition, mitochondrial genotype significantly affected multiple responses to a high-fat diet (HFD) and treatment with 17α-estradiol. Contrary to findings in mice in which males only are affected by 17α-estradiol supplementation, female rats fed a HFD beneficially responded to 17α-estradiol treatment as evidenced by declines in body mass, adiposity, and liver mass. Male rats, by contrast, differed in a mitochondrial genotype-specific manner, with only B males responding to 17α-estradiol treatment. Mitochondrial genotype and sex differences were also observed in features of brain-specific antioxidant response to a HFD and 17α-estradiol as shown by hippocampal levels of Sod2 acetylation, JNK, and FoxO3a. These results emphasize the importance of mitochondrial genotype in assessing responses to putative interventions in aging processes.
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Affiliation(s)
- Roshini Sathiaseelan
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Bumsoo Ahn
- Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Michael B Stout
- Aging & Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Oklahoma City VA Medical Center, Oklahoma City, Oklahoma, USA
| | - Sreemathi Logan
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Jonathan Wanagat
- Divisions of Geriatrics and Dermatology, Department of Medicine, University of California Los Angeles and Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, California, USA
| | - Hoang Van M Nguyen
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Norman G Hord
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Amy R Vandiver
- Divisions of Geriatrics and Dermatology, Department of Medicine, University of California Los Angeles and Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, California, USA
| | - Ramasamy Selvarani
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Rojina Ranjit
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Hannah Yarbrough
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Anthony Masingale
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Benjamin F Miller
- Aging & Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Oklahoma City VA Medical Center, Oklahoma City, Oklahoma, USA
| | - Roman F Wolf
- Oklahoma City VA Medical Center, Oklahoma City, Oklahoma, USA
| | - Steven N Austad
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Arlan Richardson
- Oklahoma City VA Medical Center, Oklahoma City, Oklahoma, USA
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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45
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Vedi M, Smith JR, Thomas Hayman G, Tutaj M, Brodie KC, De Pons JL, Demos WM, Gibson AC, Kaldunski ML, Lamers L, Laulederkind SJF, Thota J, Thorat K, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. 2022 updates to the Rat Genome Database: a Findable, Accessible, Interoperable, and Reusable (FAIR) resource. Genetics 2023; 224:iyad042. [PMID: 36930729 PMCID: PMC10474928 DOI: 10.1093/genetics/iyad042] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/19/2023] Open
Abstract
The Rat Genome Database (RGD, https://rgd.mcw.edu) has evolved from simply a resource for rat genetic markers, maps, and genes, by adding multiple genomic data types and extensive disease and phenotype annotations and developing tools to effectively mine, analyze, and visualize the available data, to empower investigators in their hypothesis-driven research. Leveraging its robust and flexible infrastructure, RGD has added data for human and eight other model organisms (mouse, 13-lined ground squirrel, chinchilla, naked mole-rat, dog, pig, African green monkey/vervet, and bonobo) besides rat to enhance its translational aspect. This article presents an overview of the database with the most recent additions to RGD's genome, variant, and quantitative phenotype data. We also briefly introduce Virtual Comparative Map (VCMap), an updated tool that explores synteny between species as an improvement to RGD's suite of tools, followed by a discussion regarding the refinements to the existing PhenoMiner tool that assists researchers in finding and comparing quantitative data across rat strains. Collectively, RGD focuses on providing a continuously improving, consistent, and high-quality data resource for researchers while advancing data reproducibility and fulfilling Findable, Accessible, Interoperable, and Reusable (FAIR) data principles.
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Affiliation(s)
- Mahima Vedi
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent C Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary L Kaldunski
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stanley J F Laulederkind
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ketaki Thorat
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Finance and Administration, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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46
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Urban LA, Li J, Gundogdu G, Trinh A, Shao H, Nguyen T, Mauney JR, Downing TL. DNA Methylation Dynamics During Esophageal Epithelial Regeneration Following Repair with Acellular Silk Fibroin Grafts in Rat. Adv Biol (Weinh) 2023; 7:e2200160. [PMID: 36658732 PMCID: PMC10401397 DOI: 10.1002/adbi.202200160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 11/10/2022] [Indexed: 01/21/2023]
Abstract
Esophageal pathologies such as atresia and benign strictures often require surgical reconstruction with autologous tissues to restore organ continuity. Complications such as donor site morbidity and limited tissue availability have spurred the development of acellular grafts for esophageal tissue replacement. Acellular biomaterials for esophageal repair rely on the activation of intrinsic regenerative mechanisms to mediate de novo tissue formation at implantation sites. Previous research has identified signaling cascades involved in neoepithelial formation in a rat model of onlay esophagoplasty with acellular silk fibroin grafts, including phosphoinositide 3-kinase (PI3K), and protein kinase B (Akt) signaling. However, it is currently unknown how these mechanisms are governed by DNA methylation (DNAme) during esophageal wound healing processes. Reduced-representation bisulfite sequencing is performed to characterize temporal DNAme dynamics in host and regenerated tissues up to 1 week postimplantation. Overall, global hypermethylation is observed at postreconstruction timepoints and an inverse correlation between promoter DNAme and the expression levels of differentially expressed proteins during regeneration. Site-specific hypomethylation targets genes associated with immune activation, while hypermethylation occurs within gene bodies encoding PI3K-Akt signaling components during the tissue remodeling period. The data provide insight into the epigenetic mechanisms during esophageal regeneration following surgical repair with acellular grafts.
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Affiliation(s)
- Lauren A. Urban
- Department of Microbiology & Molecular Genetics, University of California Irvine; Irvine, California, USA
- UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California-Irvine, Irvine, CA 92697, USA
| | - Jiachun Li
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
| | - Gokhan Gundogdu
- Department of Urology, University of California, Irvine, Orange, CA, 92868, USA
| | - Annie Trinh
- Department of Microbiology & Molecular Genetics, University of California Irvine; Irvine, California, USA
- UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California-Irvine, Irvine, CA 92697, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California-Irvine, Irvine, California 92697, USA
| | - Hanjuan Shao
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
- UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California-Irvine, Irvine, CA 92697, USA
| | - Travis Nguyen
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
| | - Joshua R. Mauney
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Urology, University of California, Irvine, Orange, CA, 92868, USA
| | - Timothy L. Downing
- Department of Microbiology & Molecular Genetics, University of California Irvine; Irvine, California, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
- UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California-Irvine, Irvine, CA 92697, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California-Irvine, Irvine, California 92697, USA
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47
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Osmanski AB, Paulat NS, Korstian J, Grimshaw JR, Halsey M, Sullivan KAM, Moreno-Santillán DD, Crookshanks C, Roberts J, Garcia C, Johnson MG, Densmore LD, Stevens RD, Rosen J, Storer JM, Hubley R, Smit AFA, Dávalos LM, Karlsson EK, Lindblad-Toh K, Ray DA. Insights into mammalian TE diversity through the curation of 248 genome assemblies. Science 2023; 380:eabn1430. [PMID: 37104570 PMCID: PMC11103246 DOI: 10.1126/science.abn1430] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 10/28/2022] [Indexed: 04/29/2023]
Abstract
We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.
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Affiliation(s)
- Austin B. Osmanski
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Nicole S. Paulat
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Jenny Korstian
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Jenna R. Grimshaw
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Michaela Halsey
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | | | | | | | - Jacquelyn Roberts
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Carlos Garcia
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Matthew G. Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | | | - Richard D. Stevens
- Department of Natural Resources Management and Natural Science Research Laboratory, Museum of Texas Tech University, Lubbock, TX, USA
| | | | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | - Liliana M. Dávalos
- Department of Ecology & Evolution, Stony Brook University, Stony Brook, NY, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
| | - Elinor K. Karlsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
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48
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Li X, Guan Z, Wang F, Wang Y, Asare E, Shi S, Lin Z, Ji T, Gao B, Song C. Evolution of piggyBac Transposons in Apoidea. INSECTS 2023; 14:402. [PMID: 37103217 PMCID: PMC10140906 DOI: 10.3390/insects14040402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 06/19/2023]
Abstract
In this study, we investigated the presence of piggyBac (PB) transposons in 44 bee genomes from the Apoidea order, which is a superfamily within the Hymenoptera, which includes a large number of bee species crucial for pollination. We annotated the PB transposons in these 44 bee genomes and examined their evolution profiles, including structural characteristics, distribution, diversity, activity, and abundance. The mined PB transposons were divided into three clades, with uneven distribution in each genus of PB transposons in Apoidea. The complete PB transposons we discovered are around 2.23-3.52 kb in length and encode transposases of approximately 580 aa, with terminal inverted repeats (TIRs) of about 14 bp and 4 bp (TTAA) target-site duplications. Long TIRs (200 bp, 201 bp, and 493 bp) were also detected in some species of bees. The DDD domains of the three transposon types were more conserved, while the other protein domains were less conserved. Generally, most PB transposons showed low abundance in the genomes of Apoidea. Divergent evolution dynamics of PB were observed in the genomes of Apoidea. PB transposons in some identified species were relatively young, whiles others were older and with some either active or inactive. In addition, multiple invasions of PB were also detected in some genomes of Apoidea. Our findings highlight the contribution of PB transposons to genomic variation in these species and suggest their potential as candidates for future gene transfer tools.
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49
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Alawadi AA, Benedito VA, Skinner RC, Warren DC, Showman C, Tou JC. RNA-sequencing revealed apple pomace ameliorates expression of genes in the hypothalamus associated with neurodegeneration in female rats fed a Western diet during adolescence to adulthood. Nutr Neurosci 2023; 26:332-344. [PMID: 35296223 DOI: 10.1080/1028415x.2022.2050008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
OBJECTIVES Apple pomace, a waste byproduct of apple processing, is rich in nutrients (e.g. polyphenols and soluble fiber) with the potential to be neuroprotective. The aim of this study was to employ RNA-sequencing (RNASeq) technology to investigate diet-gene interactions in the hypothalamus of rats after feeding a Western diet calorically substituted with apple pomace. METHODS Adolescent (age 21-29 days) female Sprague-Dawley rats were randomly assigned (n = 8 rats/group) to consume either a purified standard diet, Western (WE) diet, or Western diet calorically substituted with 10% apple pomace (WE/AP) for 8 weeks. RNA-seq was performed (n = 5 rats/group) to determine global differentially expressed genes in the hypothalamus. RESULTS RNA-seq results comparing rats fed WE to WE/AP revealed 15 differentially expressed genes in the hypothalamus. Caloric substitution of WE diet with 10% apple pomace downregulated (q < 0.06) five genes implicated in brain aging and neurodegenerative disorders: synuclein alpha, phospholipase D family member 5, NADH dehydrogenase Fe-S protein 6, choline O-acetyltransferase, and frizzled class receptor 6. DISCUSSION Altered gene expression of these five genes suggests that apple pomace ameliorated synthesis of the neurotransmitter, acetylcholine, in rats fed a WE diet. Apple pomace, a rich source of antioxidant polyphenols and soluble fiber, has been shown to reverse nonalcoholic fatty liver disease (NAFLD). Diet-induced NAFLD decreases hepatic de novo synthesis of choline, a precursor to acetylcholine. Based on preclinical evidence, apple pomace has the potential to be a sustainable functional food for maintaining brain function and for reducing the risk of neurodegeneration.
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Affiliation(s)
- Ayad A Alawadi
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, USA
| | - Vagner A Benedito
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - R Chris Skinner
- Food Systems Research Center, College of Agriculture and Life Sciences, University of Vermont Burlington, VT, USA
| | - Derek C Warren
- Division of Natural Sciences and Mathematics, University of Ozarks, Clarksville, AR, USA
| | - Casey Showman
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, USA
| | - Janet C Tou
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, USA
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50
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Richard Albert J, Kobayashi T, Inoue A, Monteagudo-Sánchez A, Kumamoto S, Takashima T, Miura A, Oikawa M, Miura F, Takada S, Hirabayashi M, Korthauer K, Kurimoto K, Greenberg MVC, Lorincz M, Kobayashi H. Conservation and divergence of canonical and non-canonical imprinting in murids. Genome Biol 2023; 24:48. [PMID: 36918927 PMCID: PMC10012579 DOI: 10.1186/s13059-023-02869-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 02/09/2023] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND Genomic imprinting affects gene expression in a parent-of-origin manner and has a profound impact on complex traits including growth and behavior. While the rat is widely used to model human pathophysiology, few imprinted genes have been identified in this murid. To systematically identify imprinted genes and genomic imprints in the rat, we use low input methods for genome-wide analyses of gene expression and DNA methylation to profile embryonic and extraembryonic tissues at allele-specific resolution. RESULTS We identify 14 and 26 imprinted genes in these tissues, respectively, with 10 of these genes imprinted in both tissues. Comparative analyses with mouse reveal that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes are conserved in the extraembryonic tissue of murids, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extraembryonic imprinting. Meta-analysis of novel imprinted genes reveals multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the appearance of ZFP57 binding motifs, and the insertion of endogenous retroviral promoters. CONCLUSIONS In summary, we provide an expanded list of imprinted loci in the rat, reveal the extent of conservation of imprinted gene expression, and identify potential mechanisms responsible for the evolution of species-specific imprinting.
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Affiliation(s)
| | - Toshihiro Kobayashi
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Azusa Inoue
- YCI Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Soichiro Kumamoto
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | | | - Asuka Miura
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Mami Oikawa
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masumi Hirabayashi
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Japan
| | - Keegan Korthauer
- Department of Statistics, University of British Columbia, Vancouver, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Nara, Japan
| | | | - Matthew Lorincz
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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