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Dong ZL, Jiao X, Wang ZG, Yuan K, Yang YQ, Wang Y, Li YT, Wang TC, Kan TY, Wang J, Tao HR. D-mannose alleviates intervertebral disc degeneration through glutamine metabolism. Mil Med Res 2024; 11:28. [PMID: 38711073 PMCID: PMC11071241 DOI: 10.1186/s40779-024-00529-4] [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: 10/21/2023] [Accepted: 04/11/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Intervertebral disc degeneration (IVDD) is a multifaceted condition characterized by heterogeneity, wherein the balance between catabolism and anabolism in the extracellular matrix of nucleus pulposus (NP) cells plays a central role. Presently, the available treatments primarily focus on relieving symptoms associated with IVDD without offering an effective cure targeting its underlying pathophysiological processes. D-mannose (referred to as mannose) has demonstrated anti-catabolic properties in various diseases. Nevertheless, its therapeutic potential in IVDD has yet to be explored. METHODS The study began with optimizing the mannose concentration for restoring NP cells. Transcriptomic analyses were employed to identify the mediators influenced by mannose, with the thioredoxin-interacting protein (Txnip) gene showing the most significant differences. Subsequently, small interfering RNA (siRNA) technology was used to demonstrate that Txnip is the key gene through which mannose exerts its effects. Techniques such as colocalization analysis, molecular docking, and overexpression assays further confirmed the direct regulatory relationship between mannose and TXNIP. To elucidate the mechanism of action of mannose, metabolomics techniques were employed to pinpoint glutamine as a core metabolite affected by mannose. Next, various methods, including integrated omics data and the Gene Expression Omnibus (GEO) database, were used to validate the one-way pathway through which TXNIP regulates glutamine. Finally, the therapeutic effect of mannose on IVDD was validated, elucidating the mechanistic role of TXNIP in glutamine metabolism in both intradiscal and orally treated rats. RESULTS In both in vivo and in vitro experiments, it was discovered that mannose has potent efficacy in alleviating IVDD by inhibiting catabolism. From a mechanistic standpoint, it was shown that mannose exerts its anti-catabolic effects by directly targeting the transcription factor max-like protein X-interacting protein (MondoA), resulting in the upregulation of TXNIP. This upregulation, in turn, inhibits glutamine metabolism, ultimately accomplishing its anti-catabolic effects by suppressing the mitogen-activated protein kinase (MAPK) pathway. More importantly, in vivo experiments have further demonstrated that compared with intradiscal injections, oral administration of mannose at safe concentrations can achieve effective therapeutic outcomes. CONCLUSIONS In summary, through integrated multiomics analysis, including both in vivo and in vitro experiments, this study demonstrated that mannose primarily exerts its anti-catabolic effects on IVDD through the TXNIP-glutamine axis. These findings provide strong evidence supporting the potential of the use of mannose in clinical applications for alleviating IVDD. Compared to existing clinically invasive or pain-relieving therapies for IVDD, the oral administration of mannose has characteristics that are more advantageous for clinical IVDD treatment.
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Affiliation(s)
- Zheng-Lin Dong
- Department of Orthopedics, Shanghai Key Laboratory of Orthopedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Xin Jiao
- Department of Orthopedics, Shanghai Key Laboratory of Orthopedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Zeng-Guang Wang
- Department of Orthopedics, Shanghai Key Laboratory of Orthopedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Kai Yuan
- Department of Orthopedics, Shanghai Key Laboratory of Orthopedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Yi-Qi Yang
- Department of Orthopedics, Shanghai Key Laboratory of Orthopedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Yao Wang
- Department of Orthopedics, Shanghai Key Laboratory of Orthopedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Yun-Tao Li
- Department of Orthopedics, Shanghai Key Laboratory of Orthopedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Tian-Chang Wang
- Department of Orthopedics, Shanghai Key Laboratory of Orthopedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Tian-You Kan
- Department of Orthopedics, Shanghai Key Laboratory of Orthopedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Jian Wang
- School of Medicine, Shanghai University, Shanghai, 200444, China.
| | - Hai-Rong Tao
- Department of Orthopedics, Shanghai Key Laboratory of Orthopedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
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Arató V, Képes Z, Szabó JP, Farkasinszky G, Sass T, Dénes N, Kis A, Opposits G, Jószai I, Kálmán FK, Hajdu I, Trencsényi G, Kertész I. Acute Myelomonoblastic Leukemia (My1/De): A Preclinical Rat Model. In Vivo 2024; 38:1064-1073. [PMID: 38688644 PMCID: PMC11059862 DOI: 10.21873/invivo.13540] [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: 01/14/2024] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND/AIM Since acute myeloid leukemias still represent the most aggressive type of adult acute leukemias, the profound understanding of disease pathology is of paramount importance for diagnostic and therapeutic purposes. Hence, this study aimed to explore the real-time disease fate with the establishment of an experimental myelomonoblastic leukemia (My1/De) rat model using preclinical positron emission tomography (PET) and whole-body autoradiography. MATERIALS AND METHODS In vitro [18F]F-FDG uptake studies were performed to compare the tracer accumulation in the newly cultured My1/De tumor cell line (blasts) with that in healthy control and My1/De bone marrow suspensions. Post transplantation of My1/De cells under the left renal capsule of Long-Evans rats, primary My1/De tumorigenesis, and metastatic propagation were investigated using [18F]F-FDG PET imaging, whole-body autoradiography and phosphorimage analyses. To assess the organ uptake profile of the tumor-carrying animals we accomplished ex vivo biodistribution studies. RESULTS The tracer accumulation in the My1/De culture cells exceeded that of both the tumorous and the healthy bone marrow suspensions (p<0.01). Based on in vivo imaging, the subrenally transplanted My1/De cells resulted in the development of leukemia in the abdominal organs, and metastasized to the mesenterial and thoracic parathymic lymph nodes (PTLNs). The lymphatic spread of metastasis was further confirmed by the significantly higher %ID/g values of the metastatic PTLNs (4.25±0.28) compared to the control (0.94±0.34). Cytochemical staining of the peripheral blood, autopsy findings, and wright-Giemsa-stained post-mortem histological sections proved the leukemic involvement of the assessed tissues/organs. CONCLUSION The currently established My1/De model appears to be well-suited for further leukemia-related therapeutic and diagnostic investigations.
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Affiliation(s)
- Viktória Arató
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Pharmaceutical Sciences, University of Debrecen, Debrecen, Hungary
| | - Zita Képes
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Debrecen, Hungary;
| | - Judit P Szabó
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gergely Farkasinszky
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tamás Sass
- Department of Surgery, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Noémi Dénes
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Adrienn Kis
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Opposits
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - István Jószai
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | | | - István Hajdu
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - György Trencsényi
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - István Kertész
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Pharmaceutical Sciences, University of Debrecen, Debrecen, Hungary
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3
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Bu W, Li Y. Advances in Immunocompetent Mouse and Rat Models. Cold Spring Harb Perspect Med 2024; 14:a041328. [PMID: 37217281 PMCID: PMC10810718 DOI: 10.1101/cshperspect.a041328] [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] [Indexed: 05/24/2023]
Abstract
Rodent models of breast cancer have played critical roles in our understanding of breast cancer development and progression as well as preclinical testing of cancer prevention and therapeutics. In this article, we first review the values and challenges of conventional genetically engineered mouse (GEM) models and newer iterations of these models, especially those with inducible or conditional regulation of oncogenes and tumor suppressors. Then, we discuss nongermline (somatic) GEM models of breast cancer with temporospatial control, made possible by intraductal injection of viral vectors to deliver oncogenes or to manipulate the genome of mammary epithelial cells. Next, we introduce the latest development in precision editing of endogenous genes using in vivo CRISPR-Cas9 technology. We conclude with the recent development in generating somatic rat models for modeling estrogen receptor-positive breast cancer, something that has been difficult to accomplish in mice.
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Affiliation(s)
- Wen Bu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yi Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
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Zhao L, Shi L, Yang Z, Zheng M, Sun Z, Sun L, Gu M, Song X, Liu G, Miao F, Wang M, Zheng S, Zhang P, Tang N, Liu K. Effect of plasma exosome lncRNA on isoproterenol hydrochloride-induced cardiotoxicity in rats. Toxicol Appl Pharmacol 2024; 484:116840. [PMID: 38307258 DOI: 10.1016/j.taap.2024.116840] [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: 11/10/2023] [Revised: 01/10/2024] [Accepted: 01/26/2024] [Indexed: 02/04/2024]
Abstract
Isoprenaline hydrochloride (IH) is a β-adrenergic receptor agonist commonly used in the treatment of hypotension, shock, asthma, and other diseases. However, IH-induced cardiotoxicity limits its application. A large number of studies have shown that long noncoding RNA (lncRNA) regulates the occurrence and development of cardiovascular diseases. This study aimed to investigate whether abnormal lncRNA expression is involved in IH-mediated cardiotoxicity. First, the Sprague-Dawley (SD) rat myocardial injury model was established. Circulating exosomes were extracted from the plasma of rats and identified. In total, 108 differentially expressed (DE) lncRNAs and 150 DE mRNAs were identified by sequencing. These results indicate that these lncRNAs and mRNAs are substantially involved in chemical cardiotoxicity. Further signaling pathway and functional studies indicated that lncRNAs and mRNAs regulate several biological processes, such as selective mRNA splicing through spliceosomes, participate in sphingolipid metabolic pathways, and play a certain role in the circulatory system. Finally, we obtained 3 upregulated lncRNAs through reverse transcription-quantitative PCR (RT-qPCR) verification and selected target lncRNA-mRNA pairs according to the regulatory relationship of lncRNA/mRNA, some of which were associated with myocardial injury. This study provides valuable insights into the role of lncRNAs as novel biomarkers of chemical-induced cardiotoxicity.
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Affiliation(s)
- Liyuan Zhao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui 230000, China; InnoStar Bio-tech Nantong Co., Ltd., Nantong, Jiangsu 226133, China; Yangtze Delta Drug Advanced Research Institute, Yangtze Delta Pharmaceutical College, Nantong, Jiangsu 226133, China
| | - Lei Shi
- Shanghai Innostar Bio-Technology Co., Ltd, China State Institute of Pharmaceutical Industry, 201203, China
| | - Zixuan Yang
- Shanghai Innostar Bio-Technology Co., Ltd, China State Institute of Pharmaceutical Industry, 201203, China
| | - Minhui Zheng
- Shanghai Innostar Bio-Technology Co., Ltd, China State Institute of Pharmaceutical Industry, 201203, China
| | - Zhimin Sun
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui 230000, China; InnoStar Bio-tech Nantong Co., Ltd., Nantong, Jiangsu 226133, China; Yangtze Delta Drug Advanced Research Institute, Yangtze Delta Pharmaceutical College, Nantong, Jiangsu 226133, China
| | - Luyao Sun
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui 230000, China; InnoStar Bio-tech Nantong Co., Ltd., Nantong, Jiangsu 226133, China; Yangtze Delta Drug Advanced Research Institute, Yangtze Delta Pharmaceutical College, Nantong, Jiangsu 226133, China
| | - Mengyun Gu
- Shanghai Innostar Bio-Technology Co., Ltd, China State Institute of Pharmaceutical Industry, 201203, China
| | - Xin Song
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui 230000, China; InnoStar Bio-tech Nantong Co., Ltd., Nantong, Jiangsu 226133, China; Yangtze Delta Drug Advanced Research Institute, Yangtze Delta Pharmaceutical College, Nantong, Jiangsu 226133, China
| | - Gang Liu
- InnoStar Bio-tech Nantong Co., Ltd., Nantong, Jiangsu 226133, China
| | - Feng Miao
- InnoStar Bio-tech Nantong Co., Ltd., Nantong, Jiangsu 226133, China
| | - Ming Wang
- InnoStar Bio-tech Nantong Co., Ltd., Nantong, Jiangsu 226133, China; Yangtze Delta Drug Advanced Research Institute, Yangtze Delta Pharmaceutical College, Nantong, Jiangsu 226133, China; Jiangxi University of Chinese Medicine, Nanchang, Jiangxi 330038, China
| | - Shaoqiu Zheng
- InnoStar Bio-tech Nantong Co., Ltd., Nantong, Jiangsu 226133, China
| | - Peng Zhang
- InnoStar Bio-tech Nantong Co., Ltd., Nantong, Jiangsu 226133, China
| | - Naping Tang
- Shanghai Innostar Bio-Technology Co., Ltd, China State Institute of Pharmaceutical Industry, 201203, China; Yangtze Delta Drug Advanced Research Institute, Yangtze Delta Pharmaceutical College, Nantong, Jiangsu 226133, China.
| | - Kelan Liu
- Intensive Care Unit, Liyang People's Hospital, Liyang, Jiangsu 213300, China.
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Chen J, Wang S, Wang D, Chiu Y, Yang N, Lian X, Zhao Z, Wei Q. Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species. Front Genet 2024; 15:1302554. [PMID: 38425715 PMCID: PMC10902437 DOI: 10.3389/fgene.2024.1302554] [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: 09/26/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction: The Tibetan antelope (Pantholops hodgsonii) is a remarkable mammal thriving in the extreme Qinghai-Tibet Plateau conditions. Despite the availability of its genome sequence, limitations in the scaffold-level assembly have hindered a comprehensive understanding of its genomics. Moreover, comparative analyses with other Bovidae species are lacking, along with insights into genome rearrangements in the Tibetan antelope. Methods: Addressing these gaps, we present a multifaceted approach by refining the Tibetan Antelope genome through linkage disequilibrium analysis with data from 15 newly sequenced samples. Results: The scaffold N50 of the refined reference is 3.2 Mbp, surpassing the previous version by 1.15-fold. Our annotation analysis resulted in 50,750 genes, encompassing 29,324 novel genes not previously study. Comparative analyses reveal 182 unique rearrangements within the scaffolds, contributing to our understanding of evolutionary dynamics and species-specific adaptations. Furthermore, by conducting detailed genomic comparisons and reconstructing rearrangements, we have successfully pioneered the reconstruction of the X-chromosome in the Tibetan antelope. Discussion: This effort enhances our comprehension of the genomic landscape of this species.
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Affiliation(s)
- Jiarui Chen
- College of Eco‐Environmental Engineering, Qinghai University, Xining, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| | - Shuwen Wang
- College of Eco‐Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Dong Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
- School of Geographical Science, Qinghai Normal University, Xining, Qinghai, China
| | - Yunkang Chiu
- Shenzhen Byoryn Technology Co., Ltd., Shenzhen, China
| | - Nan Yang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xinming Lian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, China
| | - Zicheng Zhao
- Shenzhen Byoryn Technology Co., Ltd., Shenzhen, China
| | - Qing Wei
- College of Eco‐Environmental Engineering, Qinghai University, Xining, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
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6
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Sever RE, Rosenblum LT, Reyes-Múgica M, Edwards WB, Malek MM, Kohanbash G. Survival following complete resection of neuroblastoma in novel orthotopic rat xenograft model. Sci Rep 2023; 13:20214. [PMID: 37980388 PMCID: PMC10657433 DOI: 10.1038/s41598-023-47537-3] [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: 10/02/2023] [Accepted: 11/14/2023] [Indexed: 11/20/2023] Open
Abstract
Neuroblastoma accounts for 15% of pediatric cancer deaths, despite multimodal therapy including surgical resection. Current neuroblastoma rodent models are insufficient for studying the impact of surgery and combination treatments, largely due to the small size of mouse models. Human neuroblastoma SK-N-BE(2) cells were injected into the left adrenal gland of 5-6-week-old RNU homozygous nude rats. Rats were either monitored by MRI until humane endpoint was reached or after 5 weeks underwent operative tumor resection, followed by monitoring for recurrence and survival. Following neuroblastoma cell implantation, the majority of tumors grew to greater than 5000 mm3 within 5.5-6.5 weeks, meeting the humane endpoint. Surgical resection was successfully done in 8 out of 9 rats, extending survival following tumor implantation from a median of 42 days to 78 days (p < 0.005). Pathology was consistent with human neuroblastoma, showing small round blue cell tumors with Homer-Wright rosettes, high mitoses and karyorrhectic index, and strong PHOX2B staining. Thus, we have established a novel orthotopic xenograft rat model of neuroblastoma and demonstrated increased survival of rats after surgical tumor resection. This model can be used for the development of surgical techniques, such as the use of intraoperative molecular imaging or assessment of combination therapies that include surgery.
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Affiliation(s)
- ReidAnn E Sever
- Department of Neurological Surgery, University of Pittsburgh, 530 45th Street, Pittsburgh, PA, 15201, USA
| | - Lauren Taylor Rosenblum
- Department of Surgery, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - Miguel Reyes-Múgica
- Department of Pathology, UPMC Children's Hospital of Pittsburgh, One Children's Hospital Drive, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| | - W Barry Edwards
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO, 65211, USA
| | - Marcus M Malek
- Department of Surgery, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA, 15213, USA.
- Department of Pediatric General Surgery, University of Pittsburgh, One Children's Hospital Drive, 4401 Penn Ave, Pittsburgh, PA, 15224, USA.
| | - Gary Kohanbash
- Department of Neurological Surgery, University of Pittsburgh, 530 45th Street, Pittsburgh, PA, 15201, USA.
- Department of Immunology, University of Pittsburgh Medical Center, 200 Lothrop Street, Pittsburgh, PA, 15213, USA.
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Du J, Jones T. Technical opportunities and challenges in developing total-body PET scanners for mice and rats. EJNMMI Phys 2023; 10:2. [PMID: 36592266 PMCID: PMC9807733 DOI: 10.1186/s40658-022-00523-6] [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: 12/09/2021] [Accepted: 12/20/2022] [Indexed: 01/03/2023] Open
Abstract
Positron emission tomography (PET) is the most sensitive in vivo molecular imaging technique available. Small animal PET has been widely used in studying pharmaceutical biodistribution and disease progression over time by imaging a wide range of biological processes. However, it remains true that almost all small animal PET studies using mouse or rat as preclinical models are either limited by the spatial resolution or the sensitivity (especially for dynamic studies), or both, reducing the quantitative accuracy and quantitative precision of the results. Total-body small animal PET scanners, which have axial lengths longer than the nose-to-anus length of the mouse/rat and can provide high sensitivity across the entire body of mouse/rat, can realize new opportunities for small animal PET. This article aims to discuss the technical opportunities and challenges in developing total-body small animal PET scanners for mice and rats.
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Affiliation(s)
- Junwei Du
- grid.27860.3b0000 0004 1936 9684Department of Biomedical Engineering, University of California at Davis, Davis, CA 95616 USA
| | - Terry Jones
- grid.27860.3b0000 0004 1936 9684Department of Radiology, University of California at Davis, Davis, CA 95616 USA
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8
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Moshe A, Wygoda E, Ecker N, Loewenthal G, Avram O, Israeli O, Hazkani-Covo E, Pe’er I, Pupko T. An Approximate Bayesian Computation Approach for Modeling Genome Rearrangements. Mol Biol Evol 2022; 39:msac231. [PMID: 36282896 PMCID: PMC9692237 DOI: 10.1093/molbev/msac231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024] Open
Abstract
The inference of genome rearrangement events has been extensively studied, as they play a major role in molecular evolution. However, probabilistic evolutionary models that explicitly imitate the evolutionary dynamics of such events, as well as methods to infer model parameters, are yet to be fully utilized. Here, we developed a probabilistic approach to infer genome rearrangement rate parameters using an Approximate Bayesian Computation (ABC) framework. We developed two genome rearrangement models, a basic model, which accounts for genomic changes in gene order, and a more sophisticated one which also accounts for changes in chromosome number. We characterized the ABC inference accuracy using simulations and applied our methodology to both prokaryotic and eukaryotic empirical datasets. Knowledge of genome-rearrangement rates can help elucidate their role in evolution as well as help simulate genomes with evolutionary dynamics that reflect empirical genomes.
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Affiliation(s)
- Asher Moshe
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Elya Wygoda
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noa Ecker
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gil Loewenthal
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Oren Avram
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Omer Israeli
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Einat Hazkani-Covo
- Department of Natural and Life Sciences, Open University of Israel, Ra'anana, Israel
| | - Itsik Pe’er
- Department of Computer Science, Columbia University, New York, USA
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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9
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Kille B, Balaji A, Sedlazeck FJ, Nute M, Treangen TJ. Multiple genome alignment in the telomere-to-telomere assembly era. Genome Biol 2022; 23:182. [PMID: 36038949 PMCID: PMC9421119 DOI: 10.1186/s13059-022-02735-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 07/21/2022] [Indexed: 01/22/2023] Open
Abstract
With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the computational challenge of efficiently and accurately constructing multiple genome alignments at an unprecedented scale. By identifying nucleotides across genomes which share a common ancestor, multiple genome alignments commonly serve as the bedrock for comparative genomics studies. In this review, we provide an overview of the algorithmic template that most multiple genome alignment methods follow. We also discuss prospective areas of improvement of multiple genome alignment for keeping up with continuously arriving high-quality T2T assembled genomes and for unlocking clinically-relevant insights.
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Affiliation(s)
- Bryce Kille
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Advait Balaji
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael Nute
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, TX, USA.
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10
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Xu XM, Zhang YQ, Zang FC, Lu CQ, Liu LJ, Wang J, Salvi R, Chen YC, Teng GJ. Alterations to cognitive abilities and functional networks in rats post broad-band intense noise exposure. Brain Imaging Behav 2022; 16:1884-1892. [PMID: 35543862 DOI: 10.1007/s11682-022-00643-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2022] [Indexed: 11/25/2022]
Abstract
This study aimed to investigate the alterations of cognition and functional connectivity post noise, and find the progress and neural substrates of noise induced hearing loss (NIHL)-associated cognitive impairment. We exposed rats to 122 dB broad-band noise for 2 h to induce hearing loss and the auditory function was assessed by measuring auditory brainstem response thresholds. Morris water maze test and resting state MRI were computed at 0 day, 1, 3, 6 months post noise to reveal cognitive ability and neural substrate. The interregional connections in the auditory network and default mode network, as well as the connections using the auditory cortex and cingulate cortex as seeds were also examined addtionally. The deficit in spatial learning/memory was only observed at 6 months after noise exposure. The internal connections in the auditory network and default mode network were enhanced at 0 day and decreased at 6 months post noise. The connectivity using the auditory cortex and cingulate cortex as seeds generally followed the rule of "enhancement-normal-decrease-widely decrease". A new model accounting for arousal, dementia, motor control of NIHL in is proposed. Our study highlights the fundamental flexibility of neural systems, and may also point toward novel therapeutic strategies for treating sensory disorders.
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Affiliation(s)
- Xiao-Min Xu
- Department of Radiology, Zhongda Hospital, Southeast University, No.87 Dingjiaqiao Road, Nanjing, 210009, China
- Department of Radiology, Nanjing First Hospital, Nanjing Medical University, No.68, Changle Road, Nanjing, 210006, China
| | - Yu-Qun Zhang
- School of Nursing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Feng-Chao Zang
- Department of Radiology, Zhongda Hospital, Southeast University, No.87 Dingjiaqiao Road, Nanjing, 210009, China
| | - Chun-Qiang Lu
- Department of Radiology, Zhongda Hospital, Southeast University, No.87 Dingjiaqiao Road, Nanjing, 210009, China
| | - Li-Jie Liu
- Institute of Life Sciences, Southeast University, Nanjing, China
| | - Jian Wang
- School of Human Communication Disorders, Dalhousie University, Halifax, Canada
| | - Richard Salvi
- Center for Hearing and Deafness, University at Buffalo, Buffalo, NY, 14214, USA
| | - Yu-Chen Chen
- Department of Radiology, Nanjing First Hospital, Nanjing Medical University, No.68, Changle Road, Nanjing, 210006, China.
| | - Gao-Jun Teng
- Department of Radiology, Zhongda Hospital, Southeast University, No.87 Dingjiaqiao Road, Nanjing, 210009, China.
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Song M, Zhang X, Gao Y, Wan B, Wang J, Li J, Song Y, Shen X, Wang L, Huang M, Wang X. RNA sequencing reveals the emerging role of bronchoalveolar lavage fluid exosome lncRNAs in acute lung injury. PeerJ 2022; 10:e13159. [PMID: 35378935 PMCID: PMC8976476 DOI: 10.7717/peerj.13159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/03/2022] [Indexed: 01/12/2023] Open
Abstract
Background Bronchoalveolar lavage fluid (BALF) exosomes possess different properties in different diseases, which are mediated through microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), among others. By sequencing the differentially expressed lncRNAs in BALF exosomes, we seek potential targets for the diagnosis and treatment of acute lung injury (ALI). Methods Considering that human and rat genes are about 80% similar, ALI was induced using lipopolysaccharide in six male Wistar rats, with six rats as control (all weighing 200 ± 20 g and aged 6-8 weeks). BALF exosomes were obtained 24 h after ALI. The exosomes in BALF were extracted by ultracentrifugation. The differential expression of BALF exosomal lncRNAs in BALF was analyzed by RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the functions of differentially expressed lncRNAs, which were confirmed by reverse transcription-polymerase chain reaction. Results Compared with the control group, the ALI group displayed a higher wet/dry ratio, tumor necrosis factor-α levels, and interleukin-6 levels (all P < 0.001). The airway injection of exosomes in rats led to significant infiltration by neutrophils. A total of 2,958 differentially expressed exosomal lncRNAs were identified, including 2,524 upregulated and 434 downregulated ones. Five lncRNAs confirmed the reliability of the sequencing data. The top three GO functions were phagocytic vesicle membrane, regulation of receptor biosynthesis process, and I-SMAD binding. Salmonella infection, Toll-like receptor signaling pathway, and osteoclast differentiation were the most enriched KEGG pathways. The lncRNA-miRNA interaction network of the five confirmed lncRNAs could be predicted using miRDB. Conclusions BALF-derived exosomes play an important role in ALI development and help identify potential therapeutic targets related to ALI.
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Affiliation(s)
- Meijuan Song
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiuwei Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yizhou Gao
- Department of Cardiovascular Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Bing Wan
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jinqiang Wang
- Department of Intensive Care Unit, Xuchang People’s Hospital, Xuchang, Henan, China
| | - Jinghang Li
- Department of Cardiovascular Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuanyuan Song
- Department of Cardiovascular Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaowei Shen
- Department of Cardiovascular Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Li Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Mao Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaowei Wang
- Department of Cardiovascular Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
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13
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Gonzalez Melo M, Remacle N, Cudré-Cung HP, Roux C, Poms M, Cudalbu C, Barroso M, Gersting SW, Feichtinger RG, Mayr JA, Costanzo M, Caterino M, Ruoppolo M, Rüfenacht V, Häberle J, Braissant O, Ballhausen D. The first knock-in rat model for glutaric aciduria type I allows further insights into pathophysiology in brain and periphery. Mol Genet Metab 2021; 133:157-181. [PMID: 33965309 DOI: 10.1016/j.ymgme.2021.03.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/10/2021] [Accepted: 03/30/2021] [Indexed: 02/08/2023]
Abstract
Glutaric aciduria type I (GA-I, OMIM # 231670) is an inborn error of metabolism caused by a deficiency of glutaryl-CoA dehydrogenase (GCDH). Patients develop acute encephalopathic crises (AEC) with striatal injury most often triggered by catabolic stress. The pathophysiology of GA-I, particularly in brain, is still not fully understood. We generated the first knock-in rat model for GA-I by introduction of the mutation p.R411W, the rat sequence homologue of the most common Caucasian mutation p.R402W, into the Gcdh gene of Sprague Dawley rats by CRISPR/CAS9 technology. Homozygous Gcdhki/ki rats revealed a high excretor phenotype, but did not present any signs of AEC under normal diet (ND). Exposure to a high lysine diet (HLD, 4.7%) after weaning resulted in clinical and biochemical signs of AEC. A significant increase of plasmatic ammonium concentrations was found in Gcdhki/ki rats under HLD, accompanied by a decrease of urea concentrations and a concomitant increase of arginine excretion. This might indicate an inhibition of the urea cycle. Gcdhki/ki rats exposed to HLD showed highly diminished food intake resulting in severely decreased weight gain and moderate reduction of body mass index (BMI). This constellation suggests a loss of appetite. Under HLD, pipecolic acid increased significantly in cerebral and extra-cerebral liquids and tissues of Gcdhki/ki rats, but not in WT rats. It seems that Gcdhki/ki rats under HLD activate the pipecolate pathway for lysine degradation. Gcdhki/ki rat brains revealed depletion of free carnitine, microglial activation, astroglyosis, astrocytic death by apoptosis, increased vacuole numbers, impaired OXPHOS activities and neuronal damage. Under HLD, Gcdhki/ki rats showed imbalance of intra- and extracellular creatine concentrations and indirect signs of an intracerebral ammonium accumulation. We successfully created the first rat model for GA-I. Characterization of this Gcdhki/ki strain confirmed that it is a suitable model not only for the study of pathophysiological processes, but also for the development of new therapeutic interventions. We further brought up interesting new insights into the pathophysiology of GA-I in brain and periphery.
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Affiliation(s)
- Mary Gonzalez Melo
- Pediatric Metabolic Unit, Pediatrics, Woman-Mother-Child Department, University of Lausanne and University Hospital of Lausanne, Switzerland.
| | - Noémie Remacle
- Pediatric Metabolic Unit, Pediatrics, Woman-Mother-Child Department, University of Lausanne and University Hospital of Lausanne, Switzerland
| | - Hong-Phuc Cudré-Cung
- Pediatric Metabolic Unit, Pediatrics, Woman-Mother-Child Department, University of Lausanne and University Hospital of Lausanne, Switzerland
| | - Clothilde Roux
- Service of Clinical Chemistry, University of Lausanne and University Hospital of Lausanne, Switzerland.
| | - Martin Poms
- Klinische Chemie und Biochemie Universitäts-Kinderspital Zürich, Switzerland.
| | - Cristina Cudalbu
- CIBM Center for Biomedical Imaging, Switzerland; Animal Imaging and Technology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Madalena Barroso
- University Children's Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Søren Waldemar Gersting
- University Children's Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - René Günther Feichtinger
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria.
| | - Johannes Adalbert Mayr
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria.
| | - Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; CEINGE - Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy.
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; CEINGE - Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy.
| | - Margherita Ruoppolo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; CEINGE - Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy.
| | - Véronique Rüfenacht
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland.
| | - Johannes Häberle
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland.
| | - Olivier Braissant
- Service of Clinical Chemistry, University of Lausanne and University Hospital of Lausanne, Switzerland.
| | - Diana Ballhausen
- Pediatric Metabolic Unit, Pediatrics, Woman-Mother-Child Department, University of Lausanne and University Hospital of Lausanne, Switzerland.
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Adhikary M, Mukhopadhyay K, Sarkar B. Flavonoid-rich wheatgrass (Triticum aestivum L.) diet attenuates diabetes by modulating antioxidant genes in streptozotocin-induced diabetic rats. J Food Biochem 2021; 45:e13643. [PMID: 33547672 DOI: 10.1111/jfbc.13643] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/28/2020] [Accepted: 01/21/2021] [Indexed: 01/14/2023]
Abstract
Wheatgrass, young germinated shoots of Triticum aestivum L., is proclaimed as antidiabetic nutraceutical by traditional medicines across the world. In this study, the effects of the wheatgrass diet in ameliorating oxidative stress (OS) induced during diabetes were investigated. Total phenolic and flavonoid contents (TPC and TFC) and in vitro antioxidant activity of wheatgrass extract were estimated at different days (5, 7, 9, 11, 13, and 15) after germination. Correlating the TPC and TFC with in vitro antioxidant activity, 9th DAG wheatgrass was found to possess maximum antioxidant potential. UHPLC-MS/MS analysis also revealed the presence of nine flavonoids. For in vivo studies, diabetes was induced by streptozotocin in Wistar rats fed with a high-fat diet. Concomitant administration of 9th-day wheatgrass diet (200 and 400 mg/kg) for 60 days exhibited significant improvements in hyperglycemia, body weight, lipid profile, biochemical indices (AST, ALT, GSH, GPx), and restoration of tissue architectures equivalent to normal rats. Further, qRT-PCR-based expression profiling revealed a significant modulation of major antioxidant marker genes and insulin gene which substantiated that the wheatgrass diet is effective in reducing OS during diabetes. Therefore, flavonoid-rich 9th-day wheatgrass could be used as a functional food to control diabetes. PRACTICAL APPLICATIONS: The present research supported that wheatgrass protects against oxidative stress and therefore could be utilized to ameliorate diabetes. The findings may contribute to the development and formulation of wheatgrass-based functional food or dietary supplement for diabetes by nutraceutical industries.
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Affiliation(s)
- Maria Adhikary
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, India
| | - Biswatrish Sarkar
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, India
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15
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Zinski AL, Carrion S, Michal JJ, Gartstein MA, Quock RM, Davis JF, Jiang Z. Genome-to-phenome research in rats: progress and perspectives. Int J Biol Sci 2021; 17:119-133. [PMID: 33390838 PMCID: PMC7757052 DOI: 10.7150/ijbs.51628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/06/2020] [Indexed: 01/07/2023] Open
Abstract
Because of their relatively short lifespan (<4 years), rats have become the second most used model organism to study health and diseases in humans who may live for up to 120 years. First-, second- and third-generation sequencing technologies and platforms have produced increasingly greater sequencing depth and accurate reads, leading to significant advancements in the rat genome assembly during the last 20 years. In fact, whole genome sequencing (WGS) of 47 strains have been completed. This has led to the discovery of genome variants in rats, which have been widely used to detect quantitative trait loci underlying complex phenotypes based on gene, haplotype, and sweep association analyses. DNA variants can also reveal strain, chromosome and gene functional evolutions. In parallel, phenome programs have advanced significantly in rats during the last 15 years and more than 10 databases host genome and/or phenome information. In order to discover the bridges between genome and phenome, systems genetics and integrative genomics approaches have been developed. On the other hand, multiple level information transfers from genome to phenome are executed by differential usage of alternative transcriptional start (ATS) and polyadenylation (APA) sites per gene. We used our own experiments to demonstrate how alternative transcriptome analysis can lead to enrichment of phenome-related causal pathways in rats. Development of advanced genome-to-phenome assays will certainly enhance rats as models for human biomedical research.
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Affiliation(s)
- Amy L. Zinski
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620
| | - Shane Carrion
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620
| | - Jennifer J. Michal
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620
| | - Maria A. Gartstein
- Department of Psychology, Washington State University, Pullman, WA 99164-4820
| | - Raymond M. Quock
- Department of Psychology, Washington State University, Pullman, WA 99164-4820
| | - Jon F. Davis
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99164-7620
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620
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Wang J, Zhang T, Johnston CJ, Kim SY, Gaffrey MJ, Chalupa D, Feng G, Qian WJ, McGraw MD, Ansong C. Protein thiol oxidation in the rat lung following e-cigarette exposure. Redox Biol 2020; 37:101758. [PMID: 33080441 PMCID: PMC7575796 DOI: 10.1016/j.redox.2020.101758] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/21/2020] [Accepted: 10/08/2020] [Indexed: 01/09/2023] Open
Abstract
E-cigarette (e-cig) aerosols are complex mixtures of various chemicals including humectants (propylene glycol (PG) and vegetable glycerin (VG)), nicotine, and various flavoring additives. Emerging research is beginning to challenge the "relatively safe" perception of e-cigarettes. Recent studies suggest e-cig aerosols provoke oxidative stress; however, details of the underlying molecular mechanisms remain unclear. Here we used a redox proteomics assay of thiol total oxidation to identify signatures of site-specific protein thiol modifications in Sprague-Dawley rat lungs following in vivo e-cig aerosol exposures. Histologic evaluation of rat lungs exposed acutely to e-cig aerosols revealed mild perturbations in lung structure. Bronchoalveolar lavage (BAL) fluid analysis demonstrated no significant change in cell count or differential. Conversely, total lung glutathione decreased significantly in rats exposed to e-cig aerosol compared to air controls. Redox proteomics quantified the levels of total oxidation for 6682 cysteine sites representing 2865 proteins. Protein thiol oxidation and alterations by e-cig exposure induced perturbations of protein quality control, inflammatory responses and redox homeostasis. Perturbations of protein quality control were confirmed with semi-quantification of total lung polyubiquitination and 20S proteasome activity. Our study highlights the importance of redox control in the pulmonary response to e-cig exposure and the utility of thiol-based redox proteomics as a tool for elucidating the molecular mechanisms underlying this response.
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Affiliation(s)
- Juan Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, United States
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, United States
| | - Carl J Johnston
- Department of Pediatric Pulmonology, University of Rochester Medical Center, Rochester, NY, 14642, United States
| | - So-Young Kim
- Department of Pediatric Pulmonology, University of Rochester Medical Center, Rochester, NY, 14642, United States
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, United States
| | - David Chalupa
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, 14642, United States
| | - Guanqiao Feng
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, United States.
| | - Matthew D McGraw
- Department of Pediatric Pulmonology, University of Rochester Medical Center, Rochester, NY, 14642, United States; Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, 14642, United States.
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, United States.
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Complex Structure of Lasiopodomys mandarinus vinogradovi Sex Chromosomes, Sex Determination, and Intraspecific Autosomal Polymorphism. Genes (Basel) 2020; 11:genes11040374. [PMID: 32235544 PMCID: PMC7230192 DOI: 10.3390/genes11040374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/23/2020] [Accepted: 03/27/2020] [Indexed: 11/21/2022] Open
Abstract
The mandarin vole, Lasiopodomys mandarinus, is one of the most intriguing species among mammals with non-XX/XY sex chromosome system. It combines polymorphism in diploid chromosome numbers, variation in the morphology of autosomes, heteromorphism of X chromosomes, and several sex chromosome systems the origin of which remains unexplained. Here we elucidate the sex determination system in Lasiopodomys mandarinus vinogradovi using extensive karyotyping, crossbreeding experiments, molecular cytogenetic methods, and single chromosome DNA sequencing. Among 205 karyotyped voles, one male and three female combinations of sex chromosomes were revealed. The chromosome segregation pattern and karyomorph-related reproductive performances suggested an aberrant sex determination with almost half of the females carrying neo-X/neo-Y combination. The comparative chromosome painting strongly supported this proposition and revealed the mandarin vole sex chromosome systems originated due to at least two de novo autosomal translocations onto the ancestral X chromosome. The polymorphism in autosome 2 was not related to sex chromosome variability and was proved to result from pericentric inversions. Sequencing of microdissection derived of sex chromosomes allowed the determination of the coordinates for syntenic regions but did not reveal any Y-specific sequences. Several possible sex determination mechanisms as well as interpopulation karyological differences are discussed.
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18
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Genome reorganization in different cancer types: detection of cancer specific breakpoint regions. Mol Cytogenet 2019; 12:25. [PMID: 31249626 PMCID: PMC6585066 DOI: 10.1186/s13039-019-0435-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/15/2019] [Indexed: 01/11/2023] Open
Abstract
Background Tumorigenesis is a multi-step process which is accompanied by substantial changes in genome organization. The development of these changes is not only a random process, but rather comprise specific DNA regions that are prone to the reorganization process. Results We have analyzed previously published SNP arrays from three different cancer types (pancreatic adenocarcinoma, breast cancer and metastatic melanoma) and from non-malignant control samples. We calculated segmental copy number variations as well as breakpoint regions. Some of these regions were not randomly involved in genome reorganization since we detected fifteen of them in at least 20% of all tumor samples and one region on chromosome 9 where 43% of tumors have a breakpoint. Further, the top-15 breakpoint regions show an association to known fragile sites. The relevance of these common breakpoint regions was further confirmed by analyzing SNP arrays from 917 cancer cell lines. Conclusion Our analyses suggest that genome reorganization is common in tumorigenesis and that some breakpoint regions can be found across all cancer types, while others exclusively occur in specific entities.
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19
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A novel approach to differentiate rat embryonic stem cells in vitro reveals a role for RNF12 in activation of X chromosome inactivation. Sci Rep 2019; 9:6068. [PMID: 30988473 PMCID: PMC6465393 DOI: 10.1038/s41598-019-42246-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 03/27/2019] [Indexed: 02/07/2023] Open
Abstract
X chromosome inactivation (XCI) is a mammalian specific, developmentally regulated process relying on several mechanisms including antisense transcription, non-coding RNA-mediated silencing, and recruitment of chromatin remodeling complexes. In vitro modeling of XCI, through differentiation of embryonic stem cells (ESCs), provides a powerful tool to study the dynamics of XCI, overcoming the need for embryos, and facilitating genetic modification of key regulatory players. However, to date, robust initiation of XCI in vitro has been mostly limited to mouse pluripotent stem cells. Here, we adapted existing protocols to establish a novel monolayer differentiation protocol for rat ESCs to study XCI. We show that differentiating rat ESCs properly downregulate pluripotency factor genes, and present female specific Xist RNA accumulation and silencing of X-linked genes. We also demonstrate that RNF12 seems to be an important player in regulation of initiation of XCI in rat, acting as an Xist activator. Our work provides the basis to investigate the mechanisms directing the XCI process in a model organism different from the mouse.
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Morrison JL, Berry MJ, Botting KJ, Darby JRT, Frasch MG, Gatford KL, Giussani DA, Gray CL, Harding R, Herrera EA, Kemp MW, Lock MC, McMillen IC, Moss TJ, Musk GC, Oliver MH, Regnault TRH, Roberts CT, Soo JY, Tellam RL. Improving pregnancy outcomes in humans through studies in sheep. Am J Physiol Regul Integr Comp Physiol 2018; 315:R1123-R1153. [PMID: 30325659 DOI: 10.1152/ajpregu.00391.2017] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Experimental studies that are relevant to human pregnancy rely on the selection of appropriate animal models as an important element in experimental design. Consideration of the strengths and weaknesses of any animal model of human disease is fundamental to effective and meaningful translation of preclinical research. Studies in sheep have made significant contributions to our understanding of the normal and abnormal development of the fetus. As a model of human pregnancy, studies in sheep have enabled scientists and clinicians to answer questions about the etiology and treatment of poor maternal, placental, and fetal health and to provide an evidence base for translation of interventions to the clinic. The aim of this review is to highlight the advances in perinatal human medicine that have been achieved following translation of research using the pregnant sheep and fetus.
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Affiliation(s)
- Janna L Morrison
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Mary J Berry
- Department of Paediatrics and Child Health, University of Otago , Wellington , New Zealand
| | - Kimberley J Botting
- Department of Physiology, Development, and Neuroscience, University of Cambridge , Cambridge , United Kingdom
| | - Jack R T Darby
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Martin G Frasch
- Department of Obstetrics and Gynecology, University of Washington , Seattle, Washington
| | - Kathryn L Gatford
- Robinson Research Institute and Adelaide Medical School, University of Adelaide , Adelaide, South Australia , Australia
| | - Dino A Giussani
- Department of Physiology, Development, and Neuroscience, University of Cambridge , Cambridge , United Kingdom
| | - Clint L Gray
- Department of Paediatrics and Child Health, University of Otago , Wellington , New Zealand
| | - Richard Harding
- Department of Anatomy and Developmental Biology, Monash University , Clayton, Victoria , Australia
| | - Emilio A Herrera
- Pathophysiology Program, Biomedical Sciences Institute (ICBM), Faculty of Medicine, University of Chile , Santiago , Chile
| | - Matthew W Kemp
- Division of Obstetrics and Gynecology, University of Western Australia , Perth, Western Australia , Australia
| | - Mitchell C Lock
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - I Caroline McMillen
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Timothy J Moss
- The Ritchie Centre, Hudson Institute of Medical Research, Department of Obstetrics and Gynaecology, Monash University , Clayton, Victoria , Australia
| | - Gabrielle C Musk
- Animal Care Services, University of Western Australia , Perth, Western Australia , Australia
| | - Mark H Oliver
- Liggins Institute, University of Auckland , Auckland , New Zealand
| | - Timothy R H Regnault
- Department of Obstetrics and Gynecology and Department of Physiology and Pharmacology, Western University, and Children's Health Research Institute , London, Ontario , Canada
| | - Claire T Roberts
- Robinson Research Institute and Adelaide Medical School, University of Adelaide , Adelaide, South Australia , Australia
| | - Jia Yin Soo
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Ross L Tellam
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
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Pleiman JK, Irving AA, Wang Z, Toraason E, Clipson L, Dove WF, Deming DA, Newton MA. The conserved protective cyclic AMP-phosphodiesterase function PDE4B is expressed in the adenoma and adjacent normal colonic epithelium of mammals and silenced in colorectal cancer. PLoS Genet 2018; 14:e1007611. [PMID: 30188895 PMCID: PMC6143270 DOI: 10.1371/journal.pgen.1007611] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 09/18/2018] [Accepted: 08/06/2018] [Indexed: 12/31/2022] Open
Abstract
Conservation over three mammalian genera-the mouse, rat, and human-has been found for a subset of the transcripts whose level differs between the adenoma and normal epithelium of the colon. Pde4b is one of the triply conserved transcripts whose level is enhanced both in the colonic adenoma and in the normal colonic epithelium, especially adjacent to adenomas. It encodes the phosphodiesterase PDE4B, specific for cAMP. Loss of PDE4B function in the ApcMin/+ mouse leads to a significant increase in the number of colonic adenomas. Similarly, Pde4b-deficient ApcMin/+ mice are hypersensitive to treatment by the inflammatory agent DSS, becoming moribund soon after treatment. These observations imply that the PDE4B function protects against ApcMin-induced adenomagenesis and inflammatory lethality. The paradoxical enhancement of the Pde4b transcript in the adenoma versus this inferred protective function of PDE4B can be rationalized by a feedback model in which PDE4B is first activated by early oncogenic stress involving cAMP and then, as reported for frank human colon cancer, inactivated by epigenetic silencing.
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Affiliation(s)
- Jennifer K. Pleiman
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Amy A. Irving
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Molecular and Environmental Toxicology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Zhishi Wang
- Department of Statistics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Erik Toraason
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Linda Clipson
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - William F. Dove
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Dustin A. Deming
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Division of Hematology and Medical Oncology, Department of Medicine, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Michael A. Newton
- Department of Statistics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
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22
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Mondello SE, Sunshine MD, Fischedick AE, Dreyer SJ, Horwitz GD, Anikeeva P, Horner PJ, Moritz CT. Optogenetic surface stimulation of the rat cervical spinal cord. J Neurophysiol 2018; 120:795-811. [DOI: 10.1152/jn.00461.2017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Electrical intraspinal microstimulation (ISMS) at various sites along the cervical spinal cord permits forelimb muscle activation, elicits complex limb movements and may enhance functional recovery after spinal cord injury. Here, we explore optogenetic spinal stimulation (OSS) as a less invasive and cell type-specific alternative to ISMS. To map forelimb muscle activation by OSS in rats, adeno-associated viruses (AAV) carrying the blue-light sensitive ion channels channelrhodopsin-2 (ChR2) and Chronos were injected into the cervical spinal cord at different depths and volumes. Following an AAV incubation period of several weeks, OSS-induced forelimb muscle activation and movements were assessed at 16 sites along the dorsal surface of the cervical spinal cord. Three distinct movement types were observed. We find that AAV injection volume and depth can be titrated to achieve OSS-based activation of several movements. Optical stimulation of the spinal cord is thus a promising method for dissecting the function of spinal circuitry and targeting therapies following injury. NEW & NOTEWORTHY Optogenetics in the spinal cord can be used both for therapeutic treatments and to uncover basic mechanisms of spinal cord physiology. For the first time, we describe the methodology and outcomes of optogenetic surface stimulation of the rat spinal cord. Specifically, we describe the evoked responses of forelimbs and address the effects of different adeno-associated virus injection paradigms. Additionally, we are the first to report on the limitations of light penetration through the rat spinal cord.
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Affiliation(s)
- S. E. Mondello
- Department of Rehabilitation Medicine, University of Washington, Seattle, Washington
- Center for Sensorimotor Neural Engineering, Seattle, Washington
| | - M. D. Sunshine
- Department of Rehabilitation Medicine, University of Washington, Seattle, Washington
- Center for Sensorimotor Neural Engineering, Seattle, Washington
| | - A. E. Fischedick
- Department of Rehabilitation Medicine, University of Washington, Seattle, Washington
| | - S. J. Dreyer
- Center for Sensorimotor Neural Engineering, Seattle, Washington
- Department of Bioengineering, University of Illinois, Chicago, Illinois
| | - G. D. Horwitz
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington
- Graduate Program in Neuroscience, University of Washington, Seattle, Washington
- Washington National Primate Research Center, Seattle, Washington
| | - P. Anikeeva
- Center for Sensorimotor Neural Engineering, Seattle, Washington
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - P. J. Horner
- Center for Neuroregeneration, Department of Neurological Surgery, Houston Methodist Research Institute, Houston, Texas
| | - C. T. Moritz
- Department of Rehabilitation Medicine, University of Washington, Seattle, Washington
- University of Washington Institute for Neuroengineering, University of Washington, Seattle, Washington
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington
- Graduate Program in Neuroscience, University of Washington, Seattle, Washington
- Center for Sensorimotor Neural Engineering, Seattle, Washington
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23
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Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. Genome Res 2018; 28:448-459. [PMID: 29563166 PMCID: PMC5880236 DOI: 10.1101/gr.234096.117] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/05/2018] [Indexed: 12/31/2022]
Abstract
Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.
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Affiliation(s)
- David Thybert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Maša Roller
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Fábio C P Navarro
- Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, Connecticut 06520, USA
| | - Ian Fiddes
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Christine Feig
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - David Martin-Galvez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92092, USA
| | - Václav Janoušek
- Department of Zoology, Faculty of Science, Charles University in Prague, 128 44 Prague, Czech Republic
| | - Wasiu Akanni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Sarah Aldridge
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Varshith Chakrapani
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - William Chow
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Anthony Doran
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Matthew Dunn
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Leo Goodstadt
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, United Kingdom
| | - Kerstin Howe
- Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, Connecticut 06520, USA
| | - Matthew Howell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Ambre-Aurore Josselin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Robert C Karn
- Department of Medicine, College of Medicine, University of Arizona, Tuscon, Arizona 85724, USA
| | - Christina M Laukaitis
- Department of Medicine, College of Medicine, University of Arizona, Tuscon, Arizona 85724, USA
| | - Lilue Jingtao
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Fergal Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Stefanie Nachtweide
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald 17487, Germany
| | - Michael A Quail
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Cristina Sisu
- Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, Connecticut 06520, USA
| | - Mario Stanke
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald 17487, Germany
| | - Klara Stefflova
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Cock Van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Frederic Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier/CNRS, 34095 Montpellier, France
| | - Ben Ward
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Golbahar Yazdanifar
- Department of Medicine, College of Medicine, University of Arizona, Tuscon, Arizona 85724, USA
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Mark Gerstein
- Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, Connecticut 06520, USA
| | - Benedict Paten
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Son Pham
- Bioturing Inc, San Diego, California 92121, USA
| | - Thomas M Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
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24
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Capilla L, Sánchez-Guillén RA, Farré M, Paytuví-Gallart A, Malinverni R, Ventura J, Larkin DM, Ruiz-Herrera A. Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia. Genome Biol Evol 2018; 8:3703-3717. [PMID: 28175287 PMCID: PMC5521730 DOI: 10.1093/gbe/evw276] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2016] [Indexed: 12/16/2022] Open
Abstract
Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints.
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Affiliation(s)
- Laia Capilla
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Rosa Ana Sánchez-Guillén
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Marta Farré
- Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Andreu Paytuví-Gallart
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, London, UK.,Sequentia Biotech S.L. Calle Comte d'Urgell, Barcelona, Spain
| | - Roberto Malinverni
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Denis M Larkin
- Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Aurora Ruiz-Herrera
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Sequentia Biotech S.L. Calle Comte d'Urgell, Barcelona, Spain
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25
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Gautam M, Bhattacharya I, Rai U, Majumdar SS. Hormone induced differential transcriptome analysis of Sertoli cells during postnatal maturation of rat testes. PLoS One 2018; 13:e0191201. [PMID: 29342173 PMCID: PMC5771609 DOI: 10.1371/journal.pone.0191201] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 12/30/2017] [Indexed: 11/18/2022] Open
Abstract
Sertoli cells (Sc) are unique somatic cells of testis that are the target of both FSH and testosterone (T) and regulate spermatogenesis. Although Sc of neonatal rat testes are exposed to high levels of FSH and T, robust differentiation of spermatogonial cells becomes conspicuous only after 11-days of postnatal age. We have demonstrated earlier that a developmental switch in terms of hormonal responsiveness occurs in rat Sc at around 12 days of postnatal age during the rapid transition of spermatogonia A to B. Therefore, such “functional maturation” of Sc, during pubertal development becomes prerequisite for the onset of spermatogenesis. However, a conspicuous difference in robust hormone (both T and FSH) induced gene expression during the different phases of Sc maturation restricts our understanding about molecular events necessary for the spermatogenic onset and maintenance. Here, using microarray technology, we for the first time have compared the differential transcriptional profile of Sc isolated and cultured from immature (5 days old), maturing (12 days old) and mature (60 days old) rat testes. Our data revealed that immature Sc express genes involved in cellular growth, metabolism, chemokines, cell division, MAPK and Wnt pathways, while mature Sc are more specialized expressing genes involved in glucose metabolism, phagocytosis, insulin signaling and cytoskeleton structuring. Taken together, this differential transcriptome data provide an important resource to reveal the molecular network of Sc maturation which is necessary to govern male germ cell differentiation, hence, will improve our current understanding of the etiology of some forms of idiopathic male infertility.
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Affiliation(s)
- Mukesh Gautam
- Department of Zoology, University of Delhi, Delhi, India
| | | | - Umesh Rai
- Department of Zoology, University of Delhi, Delhi, India
| | - Subeer S. Majumdar
- Cellular Endocrinology Laboratory, National Institute of Immunology, New Delhi, India
- National Institute of Animal Biotechnology, Hyderabad, India
- * E-mail:
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26
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Dess NK, Dobson K, Roberts BT, Chapman CD. Sweetener Intake by Rats Selectively Bred for Differential Saccharin Intake: Sucralose, Stevia, and Acesulfame Potassium. Chem Senses 2017; 42:381-392. [PMID: 28334357 DOI: 10.1093/chemse/bjx017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Behavioral responses to sweeteners have been used to study the evolution, mechanisms, and functions of taste. Occidental low and high saccharin consuming rats (respectively, LoS and HiS) have been selectively outbred on the basis of saccharin intake and are a valuable tool for studying variation among individuals in sweetener intake and its correlates. Relative to HiS rats, LoS rats consume smaller amounts of all nutritive and nonnutritive sweeteners tested to date, except aspartame. The lines also differ in intake of the commercial product Splenda; the roles of sucralose and saccharides in the difference are unclear. The present study extends prior work by examining intake of custom mixtures of sucralose, maltodextrin, and sugars and Splenda by LoS and HiS rats (Experiment 1A-1D), stevia and a constituent compound (rebaudioside A; Experiment 2A-2E), and acesulfame potassium tested at several concentrations or with 4 other sweeteners at one concentration each (Experiment 3A-3B). Results indicate that aversive side tastes limit intake of Splenda, stevia, and acesulfame potassium, more so among LoS rats than among HiS rats. In addition, regression analyses involving 5 sweeteners support the idea that both sweetness and bitterness are needed to account for intake of nonnutritive sweeteners, more so among LoS rats. These findings contribute to well developed and emerging literatures on sweetness and domain-general processes related to gustation.
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Affiliation(s)
- Nancy K Dess
- Department of Psychology, Occidental College, 1600 Campus Road, Los Angeles, CA 90041, USA
| | - Kiana Dobson
- Department of Psychology, Occidental College, 1600 Campus Road, Los Angeles, CA 90041, USA
| | - Brandon T Roberts
- Department of Psychology, Occidental College, 1600 Campus Road, Los Angeles, CA 90041, USA
| | - Clinton D Chapman
- Department of Psychology, Occidental College, 1600 Campus Road, Los Angeles, CA 90041, USA
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27
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DNA Length Modulates the Affinity of Fragments of Genomic DNA for the Nuclear Matrix In Vitro. J Cell Biochem 2017; 118:4487-4497. [DOI: 10.1002/jcb.26106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/01/2017] [Indexed: 01/21/2023]
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28
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Du Y, Deng W, Wang Z, Ning M, Zhang W, Zhou Y, Lo EH, Xing C. Differential subnetwork of chemokines/cytokines in human, mouse, and rat brain cells after oxygen-glucose deprivation. J Cereb Blood Flow Metab 2017; 37:1425-1434. [PMID: 27328691 PMCID: PMC5453462 DOI: 10.1177/0271678x16656199] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mice and rats are the most commonly used animals for preclinical stroke studies, but it is unclear whether targets and mechanisms are always the same across different species. Here, we mapped the baseline expression of a chemokine/cytokine subnetwork and compared responses after oxygen-glucose deprivation in primary neurons, astrocytes, and microglia from mouse, rat, and human. Baseline profiles of chemokines (CX3CL1, CXCL12, CCL2, CCL3, and CXCL10) and cytokines (IL-1α, IL-1β, IL-6, IL-10, and TNFα) showed significant differences between human and rodents. The response of chemokines/cytokines to oxygen-glucose deprivation was also significantly different between species. After 4 h oxygen-glucose deprivation and 4 h reoxygenation, human and rat neurons showed similar changes with a downregulation in many chemokines, whereas mouse neurons showed a mixed response with up- and down-regulated genes. For astrocytes, subnetwork response patterns were more similar in rats and mice compared to humans. For microglia, rat cells showed an upregulation in all chemokines/cytokines, mouse cells had many down-regulated genes, and human cells showed a mixed response with up- and down-regulated genes. This study provides proof-of-concept that species differences exist in chemokine/cytokine subnetworks in brain cells that may be relevant to stroke pathophysiology. Further investigation of differential gene pathways across species is warranted.
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Affiliation(s)
- Yang Du
- 1 Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,2 Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA.,3 Department of Geriatrics, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenjun Deng
- 4 Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zixing Wang
- 5 Departments of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - MingMing Ning
- 4 Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Wei Zhang
- 1 Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,3 Department of Geriatrics, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yiming Zhou
- 2 Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Eng H Lo
- 2 Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Changhong Xing
- 2 Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
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29
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Efficient and rapid generation of large genomic variants in rats and mice using CRISMERE. Sci Rep 2017; 7:43331. [PMID: 28266534 PMCID: PMC5339700 DOI: 10.1038/srep43331] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/24/2017] [Indexed: 01/05/2023] Open
Abstract
Modelling Down syndrome (DS) in mouse has been crucial for the understanding of the disease and the evaluation of therapeutic targets. Nevertheless, the modelling so far has been limited to the mouse and, even in this model, generating duplication of genomic regions has been labour intensive and time consuming. We developed the CRISpr MEdiated REarrangement (CRISMERE) strategy, which takes advantage of the CRISPR/Cas9 system, to generate most of the desired rearrangements from a single experiment at much lower expenses and in less than 9 months. Deletions, duplications, and inversions of genomic regions as large as 24.4 Mb in rat and mouse founders were observed and germ line transmission was confirmed for fragment as large as 3.6 Mb. Interestingly we have been able to recover duplicated regions from founders in which we only detected deletions. CRISMERE is even more powerful than anticipated it allows the scientific community to manipulate the rodent and probably other genomes in a fast and efficient manner which was not possible before.
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30
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Silva-Santiago E, Pardo JP, Hernández-Muñoz R, Aranda-Anzaldo A. The nuclear higher-order structure defined by the set of topological relationships between DNA and the nuclear matrix is species-specific in hepatocytes. Gene 2017; 597:40-48. [PMID: 27771449 DOI: 10.1016/j.gene.2016.10.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/12/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
Abstract
During the interphase the nuclear DNA of metazoan cells is organized in supercoiled loops anchored to constituents of a nuclear substructure or compartment known as the nuclear matrix. The stable interactions between DNA and the nuclear matrix (NM) correspond to a set of topological relationships that define a nuclear higher-order structure (NHOS). Current evidence suggests that the NHOS is cell-type-specific. Biophysical evidence and theoretical models suggest that thermodynamic and structural constraints drive the actualization of DNA-NM interactions. However, if the topological relationships between DNA and the NM were the subject of any biological constraint with functional significance then they must be adaptive and thus be positively selected by natural selection and they should be reasonably conserved, at least within closely related species. We carried out a coarse-grained, comparative evaluation of the DNA-NM topological relationships in primary hepatocytes from two closely related mammals: rat and mouse, by determining the relative position to the NM of a limited set of target sequences corresponding to highly-conserved genomic regions that also represent a sample of distinct chromosome territories within the interphase nucleus. Our results indicate that the pattern of topological relationships between DNA and the NM is not conserved between the hepatocytes of the two closely related species, suggesting that the NHOS, like the karyotype, is species-specific.
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Affiliation(s)
- Evangelina Silva-Santiago
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, 50180, Edo. Méx., Mexico
| | - Juan Pablo Pardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacan, 04510, Ciudad de México, Mexico
| | - Rolando Hernández-Muñoz
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacan, 04510, Ciudad de México, Mexico
| | - Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, 50180, Edo. Méx., Mexico.
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31
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Giménez MD, Panithanarak T, Hauffe HC, Searle JB. Empirical demonstration of hybrid chromosomal races in house mice. Evolution 2016; 70:1651-8. [PMID: 27287407 DOI: 10.1111/evo.12970] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/02/2016] [Accepted: 05/24/2016] [Indexed: 11/29/2022]
Abstract
Western house mice (Mus musculus domesticus) and common shrews (Sorex araneus) are important models for study of chromosomal speciation. Both had ancestral karyotypes consisting of telocentric chromosomes, and each is subdivided into numerous chromosomal races many of which have resulted from fixation of new mutations (Robertsonian fusions and whole-arm reciprocal translocations). However, some chromosomal races in both species may alternatively have originated through hybridization, with particular homozygous recombinant products reaching fixation. Here, we demonstrate the process of generation of hybrid chromosomal races for the first time in either species using molecular markers. Analysis of centromeric microsatellite markers show that the Mid Valtellina (IMVA) and Upper Valtellina (IUVA) chromosomal races of the house mouse are recombinant products of hybridization of the Lower Valtellina (ILVA) and Poschiavo (CHPO) chromosomal races, supporting earlier theoretical analysis. IMVA and IUVA occupy a small area of the Italian Alps where ILVA makes contact with CHPO. IUVA and CHPO have previously been shown to be reproductively isolated in one village, emphasizing that hybrid chromosomal races in small mammals, as in plants, have the potential to be part of the speciation process.
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Affiliation(s)
- Mabel D Giménez
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom.,Instituto de Biología Subtropical (CONICET - UNaM), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Félix de Azara 1552, N3300LQH Posadas, Misiones, Argentina
| | - Thadsin Panithanarak
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom.,Institute of Marine Science, Burapha University, Chonburi, Thailand
| | - Heidi C Hauffe
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom.,Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Jeremy B Searle
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom. .,Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, New York, 14853-2701.
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Lyte M, Fodor AA, Chapman CD, Martin GG, Perez-Chanona E, Jobin C, Dess NK. Gut Microbiota and a Selectively Bred Taste Phenotype: A Novel Model of Microbiome-Behavior Relationships. Psychosom Med 2016; 78:610-9. [PMID: 27035357 DOI: 10.1097/psy.0000000000000318] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVES The microbiota-gut-brain axis is increasingly implicated in obesity, anxiety, stress, and other health-related processes. Researchers have proposed that gut microbiota may influence dietary habits, and pathways through the microbiota-gut-brain axis make such a relationship feasible; however, few data bear on the hypothesis. As a first step in the development of a model system, the gut microbiome was examined in rat lines selectively outbred on a taste phenotype with biobehavioral profiles that have diverged with respect to energy regulation, anxiety, and stress. METHODS Occidental low and high-saccharin-consuming rats were assessed for body mass and chow, water, and saccharin intake; littermate controls had shared cages with rats in the experimental group but were not assessed. Cecum and colon microbial communities were profiled using Illumina 16S rRNA sequencing and multivariate analysis of microbial diversity and composition. RESULTS The saccharin phenotype was confirmed (low-saccharin-consuming rats, 0.7Δ% [0.9Δ%]; high-saccharin-consuming rats, 28.1Δ% [3.6Δ%]). Regardless of saccharin exposure, gut microbiota differed between lines in terms of overall community similarity and taxa at lower phylogenetic levels. Specifically, 16 genera in three phyla distinguished the lines at a 10% false discovery rate. DISCUSSION The study demonstrates for the first time that rodent lines created through selective pressure on taste and differing on functionally related correlates host different microbial communities. Whether the microbiota are causally related to the taste phenotype or its correlates remains to be determined. These findings encourage further inquiry on the relationship of the microbiome to taste, dietary habits, emotion, and health.
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Affiliation(s)
- Mark Lyte
- From the Department of Veterinary Microbiology and Preventive Medicine, School of Veterinary Medicine (Lyte), Iowa State University, Ames, Iowa; Department of Immunotherapeutics and Biotechnology (Lyte), Texas Tech University Health Sciences Center, Abilene, Texas; Department of Bioinformatics and Genomics (Fodor), University of North Carolina at Charlotte, North Carolina; School of Medicine (Perez-Chanona), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Division of Gastroenterology, Department of Medicine (Jobin), University of Florida College of Medicine, Gainesville, Florida; and Occidental College (Chapman, Martin, Dess), Los Angeles, California
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Xing C, Lo EH. Help-me signaling: Non-cell autonomous mechanisms of neuroprotection and neurorecovery. Prog Neurobiol 2016; 152:181-199. [PMID: 27079786 DOI: 10.1016/j.pneurobio.2016.04.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 04/06/2016] [Accepted: 04/09/2016] [Indexed: 12/11/2022]
Abstract
Self-preservation is required for life. At the cellular level, this fundamental principle is expressed in the form of molecular mechanisms for preconditioning and tolerance. When the cell is threatened, internal cascades of survival signaling become triggered to protect against cell death and defend against future insults. Recently, however, emerging findings suggest that this principle of self-preservation may involve not only intracellular signals; the release of extracellular signals may provide a way to recruit adjacent cells into an amplified protective program. In the central nervous system where multiple cell types co-exist, this mechanism would allow threatened neurons to "ask for help" from glial and vascular compartments. In this review, we describe this new concept of help-me signaling, wherein damaged or diseased neurons release signals that may shift glial and vascular cells into potentially beneficial phenotypes, and help remodel the neurovascular unit. Understanding and dissecting these non-cell autonomous mechanisms of self-preservation in the CNS may lead to novel opportunities for neuroprotection and neurorecovery.
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Affiliation(s)
- Changhong Xing
- Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
| | - Eng H Lo
- Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
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Pradhan BS, Majumdar SS. An Efficient Method for Generation of Transgenic Rats Avoiding Embryo Manipulation. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e293. [PMID: 27111419 PMCID: PMC5014465 DOI: 10.1038/mtna.2016.9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 01/07/2016] [Indexed: 12/20/2022]
Abstract
Although rats are preferred over mice as an animal model, transgenic animals are generated predominantly using mouse embryos. There are limitations in the generation of transgenic rat by embryo manipulation. Unlike mouse embryos, most of the rat embryos do not survive after male pronuclear DNA injection which reduces the efficiency of generation of transgenic rat by this method. More importantly, this method requires hundreds of eggs collected by killing several females for insertion of transgene to generate transgenic rat. To this end, we developed a noninvasive and deathless technique for generation of transgenic rats by integrating transgene into the genome of the spermatogonial cells by testicular injection of DNA followed by electroporation. After standardization of this technique using EGFP as a transgene, a transgenic disease model displaying alpha thalassemia was successfully generated using rats. This efficient method will ease the generation of transgenic rats without killing the lives of rats while simultaneously reducing the number of rats used for generation of transgenic animal.
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Affiliation(s)
- Bhola Shankar Pradhan
- Cellular Endocrinology Laboratory, National Institute of Immunology, New Delhi, India
| | - Subeer S Majumdar
- Cellular Endocrinology Laboratory, National Institute of Immunology, New Delhi, India
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Sangpakdee W, Tanomtong A, Fan X, Pinthong K, Weise A, Liehr T. Application of multicolor banding combined with heterochromatic and locus-specific probes identify evolutionary conserved breakpoints in Hylobates pileatus. Mol Cytogenet 2016; 9:17. [PMID: 26893612 PMCID: PMC4758170 DOI: 10.1186/s13039-016-0228-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 02/10/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The question what makes Homo sapiens sapiens (HSA) special among other species is one of the basic questions of mankind. A small contribution to answer this question is to study the chromosomal constitution of HSA compared to other, closely related species. In order to check the types and extent of evolutionary conserved breakpoints we studied here for the first time the chromosomes of Hylobates pileatus (HPI) compared to HSA and Hylobates lar (HLA) by means of molecular cytogenetics. RESULTS Overall, 68 new evolutionary conserved breakpoints compared to HSA could be characterized in this study. Interestingly, only seven of those were different compared to HLA. However, application of heterochromatic human DNA-probes provided evidence that observed high chromosomal rearrangement rates of gibbons in HPI happened rather in these repetitive elements than in euchromatin, even though most centromeric positions were preserved in HPI compared to HSA. CONCLUSION Understanding genomes of other species and comparing them to HSA needs full karyotypic and high resolution genomic data to approach both: euchromatic and heterochromatic regions of the studied chromosome-content. This study provides full karyotypic data and previously not available data on heterochromatin-syntenies of HPI and HSA.
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Affiliation(s)
- Wiwat Sangpakdee
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany ; Department of Biology Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Muang District, Khon Kaen, 40002 Thailand
| | - Alongklod Tanomtong
- Department of Biology Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Muang District, Khon Kaen, 40002 Thailand
| | - Xiaobo Fan
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Krit Pinthong
- Faculty of Science and Technology, Surindra Rajabhat University, 186 Moo 1, Maung District, Surin, 32000 Thailand
| | - Anja Weise
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
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Celik O, Aydin S, Celik N, Yilmaz M. Ghrelin has both indirect and direct inhibiting effect on GnRH neurons: Reply for letter to editor "Ghrelin directly affects GnRH neurons". Peptides 2016; 75:118-20. [PMID: 26589189 DOI: 10.1016/j.peptides.2015.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 10/16/2015] [Accepted: 10/27/2015] [Indexed: 11/16/2022]
Affiliation(s)
- Onder Celik
- Department of Obstetrics and Gynecology, Usak, Turkey.
| | - Suleyman Aydin
- Firat University, School of Medicine, Department of Medical Biochemistry (Firat Hormones Research Group), 23119 Elazig, Turkey.
| | - Nilufer Celik
- Behcet Uz Children's Hospital, Department of Biochemistry, Izmir, Turkey
| | - Musa Yilmaz
- Firat University, School of Medicine, Department of Medical Biochemistry (Firat Hormones Research Group) 23119 Elazig, Turkey
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Jiminez JA, Uwiera TC, Douglas Inglis G, Uwiera RRE. Animal models to study acute and chronic intestinal inflammation in mammals. Gut Pathog 2015; 7:29. [PMID: 26561503 PMCID: PMC4641401 DOI: 10.1186/s13099-015-0076-y] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/22/2015] [Indexed: 02/06/2023] Open
Abstract
Acute and chronic inflammatory diseases of the intestine impart a significant and negative impact on the health and well-being of human and non-human mammalian animals. Understanding the underlying mechanisms of inflammatory disease is mandatory to develop effective treatment and prevention strategies. As inflammatory disease etiologies are multifactorial, the use of appropriate animal models and associated metrics of disease are essential. In this regard, animal models used alone or in combination to study acute and chronic inflammatory disease of the mammalian intestine paired with commonly used inflammation-inducing agents are reviewed. This includes both chemical and biological incitants of inflammation, and both non-mammalian (i.e. nematodes, insects, and fish) and mammalian (i.e. rodents, rabbits, pigs, ruminants, dogs, and non-human primates) models of intestinal inflammation including germ-free, gnotobiotic, as well as surgical, and genetically modified animals. Importantly, chemical and biological incitants induce inflammation via a multitude of mechanisms, and intestinal inflammation and injury can vary greatly according to the incitant and animal model used, allowing studies to ascertain both long-term and short-term effects of inflammation. Thus, researchers and clinicians should be aware of the relative strengths and limitations of the various animal models used to study acute and chronic inflammatory diseases of the mammalian intestine, and the scope and relevance of outcomes achievable based on this knowledge. The ability to induce inflammation to mimic common human diseases is an important factor of a successful animal model, however other mechanisms of disease such as the amount of infective agent to induce disease, invasion mechanisms, and the effect various physiologic changes can have on inducing damage are also important features. In many cases, the use of multiple animal models in combination with both chemical and biological incitants is necessary to answer the specific question being addressed regarding intestinal disease. Some incitants can induce acute responses in certain animal models while others can be used to induce chronic responses; this review aims to illustrate the strengths and weaknesses in each animal model and to guide the choice of an appropriate acute or chronic incitant to facilitate intestinal disease.
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Affiliation(s)
- Janelle A. Jiminez
- />Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB Canada
- />Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Trina C. Uwiera
- />Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB Canada
| | - G. Douglas Inglis
- />Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB Canada
| | - Richard R. E. Uwiera
- />Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
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Berthelot C, Muffato M, Abecassis J, Roest Crollius H. The 3D organization of chromatin explains evolutionary fragile genomic regions. Cell Rep 2015; 10:1913-24. [PMID: 25801028 DOI: 10.1016/j.celrep.2015.02.046] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 12/17/2014] [Accepted: 02/18/2015] [Indexed: 10/23/2022] Open
Abstract
Genomic rearrangements are a major source of evolutionary divergence in eukaryotic genomes, a cause of genetic diseases and a hallmark of tumor cell progression, yet the mechanisms underlying their occurrence and evolutionary fixation are poorly understood. Statistical associations between breakpoints and specific genomic features suggest that genomes may contain elusive “fragile regions” with a higher propensity for breakage. Here, we use ancestral genome reconstructions to demonstrate a near-perfect correlation between gene density and evolutionary rearrangement breakpoints. Simulations based on functional features in the human genome show that this pattern is best explained as the outcome of DNA breaks that occur in open chromatin regions coming into 3D contact in the nucleus. Our model explains how rearrangements reorganize the order of genes in an evolutionary neutral fashion and provides a basis for understanding the susceptibility of “fragile regions” to breakage.
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Celik O, Celik N, Gungor S, Haberal ET, Aydin S. Selective Regulation of Oocyte Meiotic Events Enhances Progress in Fertility Preservation Methods. BIOCHEMISTRY INSIGHTS 2015; 8:11-21. [PMID: 26417205 PMCID: PMC4577271 DOI: 10.4137/bci.s28596] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/23/2015] [Accepted: 08/24/2015] [Indexed: 11/15/2022]
Abstract
Following early embryonic germ cell migration, oocytes are surrounded by somatic cells and remain arrested at diplotene stage until luteinizing hormone (LH) surge. Strict regulation of both meiotic arrest and meiotic resumption during dormant stage are critical for future fertility. Inter-cellular signaling system between the somatic compartment and oocyte regulates these meiotic events and determines the follicle quality. As well as the collected number of eggs, their qualities are also important for in vitro fertilization (IVF) outcome. In spontaneous and IVF cycles, germinal vesicle (GV)–stage oocytes, premature GV breakdown, and persistence of first meiotic arrest limit the reproductive performance. Likewise, both women with premature ovarian aging and young cancer women are undergoing chemoradiotherapy under the risk of follicle loss because of unregulated meiotic events. Understanding of oocyte meiotic events is therefore critical for the prevention of functional ovarian reserve. High levels of cyclic guanosine monophophate (cGMP), cyclic adenosine monophophate (cAMP) and low phosphodiesterase (PDE) 3A enzyme activity inside the oocyte are responsible for maintaining of meiotic arrest before the LH surge. cGMP is produced in the somatic compartment, and natriuretic peptide precursor C (Nppc) and natriuretic peptide receptor 2 (Npr2) regulate its production. cGMP diffuses into the oocyte and reduces the PDE3A activity, which inhibits the conversion of cAMP to the 5′AMP, and cAMP levels are enhanced. In addition, oocyte itself has the ability to produce cAMP. Taken together, accumulation of cAMP inside the oocyte induces protein kinase activity, which leads to the inhibition of maturation-promoting factor and meiotic arrest also continues. By stimulating the expression of epidermal growth factor, LH inhibits the Nppc/Npr2 system, blocks cGMP synthesis, and initiates meiotic resumption. Oocytes lacking the functional of this pathway may lead to persistence of the GV oocyte, which reduces the number of good quality eggs. Selective regulation of somatic cell signals and oocyte meiotic events enhance progress in fertility preservation methods, which may give us the opportunity to prevent follicle loss in prematurely aging women and young women with cancer are undergoing chemoradiotherapy.
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Affiliation(s)
- Onder Celik
- Private Clinic, Obstetrics and Gynecology, Usak, Turkey
| | - Nilufer Celik
- Behçet Uz Children's Hospital, Department of Biochemistry, İzmir, Turkey
| | - Sami Gungor
- Private Medical Hospital, Obstetrics and Gynecology, Elazig, Turkey
| | - Esra Tustas Haberal
- Umraniye Education and Research Hospital, Obstetrics and Gynecology, İstanbul, Turkey
| | - Suleyman Aydin
- Department of Medical Biochemistry (Firat Hormone Research Group), School of Medicine, Firat University, Elazig, Turkey
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Weise A, Kosyakova N, Voigt M, Aust N, Mrasek K, Löhmer S, Rubtsov N, Karamysheva TV, Trifonov VA, Hardekopf D, Jančušková T, Pekova S, Wilhelm K, Liehr T, Fan X. Comprehensive Analyses of White-Handed Gibbon Chromosomes Enables Access to 92 Evolutionary Conserved Breakpoints Compared to the Human Genome. Cytogenet Genome Res 2015; 145:42-9. [PMID: 25926034 DOI: 10.1159/000381764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2015] [Indexed: 11/19/2022] Open
Abstract
Gibbon species (Hylobatidae) impress with an unusually high number of numerical and structural chromosomal changes within the family itself as well as compared to other Hominoidea including humans. In former studies applying molecular cytogenetic methods, 86 evolutionary conserved breakpoints (ECBs) were reported in the white-handed gibbon (Hylobates lar, HLA) with respect to the human genome. To analyze those ECBs in more detail and also to achieve a better understanding of the fast karyotype evolution in Hylobatidae, molecular data for these regions are indispensably necessary. In the present study, we obtained whole chromosome-specific probes by microdissection of all 21 HLA autosomes and prepared them for aCGH. Locus-specific DNA probes were also used for further molecular cytogenetic characterization of selected regions. Thus, we could map 6 yet unreported ECBs in HLA with respect to the human genome. Additionally, in 26 of the 86 previously reported ECBs, the present approach enabled a more precise breakpoint mapping. Interestingly, a preferred localization of ECBs within segmental duplications, copy number variant regions, and fragile sites was observed.
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Affiliation(s)
- Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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Veerappa AM, Vishweswaraiah S, Lingaiah K, Murthy M, Suresh RV, Manjegowda DS, Ramachandra NB. Global spectrum of copy number variations reveals genome organizational plasticity and proposes new migration routes. PLoS One 2015; 10:e0121846. [PMID: 25909454 PMCID: PMC4409114 DOI: 10.1371/journal.pone.0121846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 02/16/2015] [Indexed: 11/19/2022] Open
Abstract
Global spectrum of CNVs is required to catalog variations to provide a high-resolution on the dynamics of genome-organization and human migration. In this study, we performed genome-wide genotyping using high-resolution arrays and identified 44,109 CNVs from 1,715 genomes across 12 populations. The study unraveled the force of independent evolutionary dynamics on genome-organizational plasticity across populations. We demonstrated the use of CNV tool to study human migration and identified a second major settlement establishing new migration routes in addition to existing ones.
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Affiliation(s)
- Avinash M. Veerappa
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore-06, Karnataka, India
| | - Sangeetha Vishweswaraiah
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore-06, Karnataka, India
| | - Kusuma Lingaiah
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore-06, Karnataka, India
| | - Megha Murthy
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore-06, Karnataka, India
| | - Raviraj V. Suresh
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore-06, Karnataka, India
| | - Dinesh S. Manjegowda
- NUCSER, KS Hegde Medical Academy, Nitte University, Mangalore-18, Karnataka, India
| | - Nallur B. Ramachandra
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore-06, Karnataka, India
- * E-mail:
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Gerber PA, Buhren BA, Schrumpf H, Homey B, Zlotnik A, Hevezi P. The top skin-associated genes: a comparative analysis of human and mouse skin transcriptomes. Biol Chem 2014; 395:577-91. [PMID: 24497224 DOI: 10.1515/hsz-2013-0279] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/30/2014] [Indexed: 11/15/2022]
Abstract
The mouse represents a key model system for the study of the physiology and biochemistry of skin. Comparison of skin between mouse and human is critical for interpretation and application of data from mouse experiments to human disease. Here, we review the current knowledge on structure and immunology of mouse and human skin. Moreover, we present a systematic comparison of human and mouse skin transcriptomes. To this end, we have recently used a genome-wide database of human gene expression to identify genes highly expressed in skin, with no, or limited expression elsewhere - human skin-associated genes (hSAGs). Analysis of our set of hSAGs allowed us to generate a comprehensive molecular characterization of healthy human skin. Here, we used a similar database to generate a list of mouse skin-associated genes (mSAGs). A comparative analysis between the top human (n=666) and mouse (n=873) skin-associated genes (SAGs) revealed a total of only 30.2% identity between the two lists. The majority of shared genes encode proteins that participate in structural and barrier functions. Analysis of the top functional annotation terms revealed an overlap for morphogenesis, cell adhesion, structure, and signal transduction. The results of this analysis, discussed in the context of published data, illustrate the diversity between the molecular make up of skin of both species and grants a probable explanation, why results generated in murine in vivo models often fail to translate into the human.
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Irving AA, Yoshimi K, Hart ML, Parker T, Clipson L, Ford MR, Kuramoto T, Dove WF, Amos-Landgraf JM. The utility of Apc-mutant rats in modeling human colon cancer. Dis Model Mech 2014; 7:1215-25. [PMID: 25288683 PMCID: PMC4213726 DOI: 10.1242/dmm.016980] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Prior to the advent of genetic engineering in the mouse, the rat was the model of choice for investigating the etiology of cancer. Now, recent advances in the manipulation of the rat genome, combined with a growing recognition of the physiological differences between mice and rats, have reignited interest in the rat as a model of human cancer. Two recently developed rat models, the polyposis in the rat colon (Pirc) and Kyoto Apc Delta (KAD) strains, each carry mutations in the intestinal-cancer-associated adenomatous polyposis coli (Apc) gene. In contrast to mouse models carrying Apc mutations, in which cancers develop mainly in the small intestine rather than in the colon and there is no gender bias, these rat models exhibit colonic predisposition and gender-specific susceptibility, as seen in human colon cancer. The rat also provides other experimental resources as a model organism that are not provided by the mouse: the structure of its chromosomes facilitates the analysis of genomic events, the size of its colon permits longitudinal analysis of tumor growth, and the size of biological samples from the animal facilitates multiplexed molecular analyses of the tumor and its host. Thus, the underlying biology and experimental resources of these rat models provide important avenues for investigation. We anticipate that advances in disease modeling in the rat will synergize with resources that are being developed in the mouse to provide a deeper understanding of human colon cancer.
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Affiliation(s)
- Amy A Irving
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Kazuto Yoshimi
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Marcia L Hart
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Taybor Parker
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Linda Clipson
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Madeline R Ford
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Takashi Kuramoto
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - William F Dove
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - James M Amos-Landgraf
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, WI 53792, USA. Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA.
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Abstract
Pseudogenes are degraded fossil copies of genes. Here, we report a comparison of pseudogenes spanning three phyla, leveraging the completed annotations of the human, worm, and fly genomes, which we make available as an online resource. We find that pseudogenes are lineage specific, much more so than protein-coding genes, reflecting the different remodeling processes marking each organism's genome evolution. The majority of human pseudogenes are processed, resulting from a retrotranspositional burst at the dawn of the primate lineage. This burst can be seen in the largely uniform distribution of pseudogenes across the genome, their preservation in areas with low recombination rates, and their preponderance in highly expressed gene families. In contrast, worm and fly pseudogenes tell a story of numerous duplication events. In worm, these duplications have been preserved through selective sweeps, so we see a large number of pseudogenes associated with highly duplicated families such as chemoreceptors. However, in fly, the large effective population size and high deletion rate resulted in a depletion of the pseudogene complement. Despite large variations between these species, we also find notable similarities. Overall, we identify a broad spectrum of biochemical activity for pseudogenes, with the majority in each organism exhibiting varying degrees of partial activity. In particular, we identify a consistent amount of transcription (∼15%) across all species, suggesting a uniform degradation process. Also, we see a uniform decay of pseudogene promoter activity relative to their coding counterparts and identify a number of pseudogenes with conserved upstream sequences and activity, hinting at potential regulatory roles.
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A high resolution map of mammalian X chromosome fragile regions assessed by large-scale comparative genomics. Mamm Genome 2014; 25:618-35. [PMID: 25086724 DOI: 10.1007/s00335-014-9537-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 07/14/2014] [Indexed: 10/24/2022]
Abstract
Chromosomal evolution involves multiple changes at structural and numerical levels. These changes, which are related to the variation of the gene number and their location, can be tracked by the identification of syntenic blocks (SB). First reports proposed that ~180-280 SB might be shared by mouse and human species. More recently, further studies including additional genomes have identified up to ~1,400 SB during the evolution of eutherian species. A considerable number of studies regarding the X chromosome's structure and evolution have been undertaken because of its extraordinary biological impact on reproductive fitness and speciation. Some have identified evolutionary breakpoint regions and fragile sites at specific locations in the human X chromosome. However, mapping these regions to date has involved using low-to-moderate resolution techniques. Such scenario might be related to underestimating their total number and giving an inaccurate location. The present study included using a combination of bioinformatics methods for identifying, at base-pair level, chromosomal rearrangements occurring during X chromosome evolution in 13 mammalian species. A comparative technique using four different algorithms was used for optimizing the detection of hotspot regions in the human X chromosome. We identified a significant interspecific variation in SB size which was related to genetic information gain regarding the human X chromosome. We found that human hotspot regions were enriched by LINE-1 and Alu transposable elements, which may have led to intraspecific chromosome rearrangement events. New fragile regions located in the human X chromosome have also been postulated. We estimate that the high resolution map of X chromosome fragile sites presented here constitutes useful data concerning future studies on mammalian evolution and human disease.
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Antonic A, Dottori M, Leung J, Sidon K, Batchelor PE, Wilson W, Macleod MR, Howells DW. Hypothermia protects human neurons. Int J Stroke 2014; 9:544-52. [PMID: 24393199 PMCID: PMC4235397 DOI: 10.1111/ijs.12224] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 10/14/2013] [Indexed: 12/23/2022]
Abstract
BACKGROUND AND AIMS Hypothermia provides neuroprotection after cardiac arrest, hypoxic-ischemic encephalopathy, and in animal models of ischemic stroke. However, as drug development for stroke has been beset by translational failure, we sought additional evidence that hypothermia protects human neurons against ischemic injury. METHODS Human embryonic stem cells were cultured and differentiated to provide a source of neurons expressing β III tubulin, microtubule-associated protein 2, and the Neuronal Nuclei antigen. Oxygen deprivation, oxygen-glucose deprivation, and H2 O2 -induced oxidative stress were used to induce relevant injury. RESULTS Hypothermia to 33°C protected these human neurons against H2 O2 -induced oxidative stress reducing lactate dehydrogenase release and Terminal deoxynucleotidyl transferase dUTP nick end labeling-staining by 53% (P ≤ 0·0001; 95% confidence interval 34·8-71·04) and 42% (P ≤ 0·0001; 95% confidence interval 27·5-56·6), respectively, after 24 h in culture. Hypothermia provided similar protection against oxygen-glucose deprivation (42%, P ≤ 0·001, 95% confidence interval 18·3-71·3 and 26%, P ≤ 0·001; 95% confidence interval 12·4-52·2, respectively) but provided no protection against oxygen deprivation alone. Protection (21%) persisted against H2 O2 -induced oxidative stress even when hypothermia was initiated six-hours after onset of injury (P ≤ 0·05; 95% confidence interval 0·57-43·1). CONCLUSION We conclude that hypothermia protects stem cell-derived human neurons against insults relevant to stroke over a clinically relevant time frame. Protection against H2 O2 -induced injury and combined oxygen and glucose deprivation but not against oxygen deprivation alone suggests an interaction in which protection benefits from reduction in available glucose under some but not all circumstances.
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Affiliation(s)
- Ana Antonic
- Florey Institute of Neuroscience and Mental HealthHeidelberg, Vic, Australia
- Department of Medicine, University of MelbourneHeidelberg, Vic, Australia
| | - Mirella Dottori
- Centre for Neuroscience Research, Department of Anatomy and Neuroscience, University of MelbourneMelbourne, Vic, Australia
| | - Jessie Leung
- Centre for Neuroscience Research, Department of Anatomy and Neuroscience, University of MelbourneMelbourne, Vic, Australia
| | - Kate Sidon
- Florey Institute of Neuroscience and Mental HealthHeidelberg, Vic, Australia
- Department of Medicine, University of MelbourneHeidelberg, Vic, Australia
| | - Peter E Batchelor
- Department of Medicine, University of MelbourneHeidelberg, Vic, Australia
| | - William Wilson
- CSIRO Mathematics, Informatics and Statistics, Riverside Life Sciences PrecinctNorth Ryde, NSW, Australia
| | - Malcolm R Macleod
- Department of Clinical Neurosciences, Western General Hospital, University of EdinburghEdinburgh, UK
| | - David W Howells
- Florey Institute of Neuroscience and Mental HealthHeidelberg, Vic, Australia
- Department of Medicine, University of MelbourneHeidelberg, Vic, Australia
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Abstract
Bacterial artificial chromosome (BAC) physical maps embedding a large number of BAC end sequences (BESs) were generated for Oryza sativa ssp. indica varieties Minghui 63 (MH63) and Zhenshan 97 (ZS97) and were compared with the genome sequences of O. sativa spp. japonica cv. Nipponbare and O. sativa ssp. indica cv. 93-11. The comparisons exhibited substantial diversities in terms of large structural variations and small substitutions and indels. Genome-wide BAC-sized and contig-sized structural variations were detected, and the shared variations were analyzed. In the expansion regions of the Nipponbare reference sequence, in comparison to the MH63 and ZS97 physical maps, as well as to the previously constructed 93-11 physical map, the amounts and types of the repeat contents, and the outputs of gene ontology analysis, were significantly different from those of the whole genome. Using the physical maps of four wild Oryza species from OMAP (http://www.omap.org) as a control, we detected many conserved and divergent regions related to the evolution process of O. sativa. Between the BESs of MH63 and ZS97 and the two reference sequences, a total of 1532 polymorphic simple sequence repeats (SSRs), 71,383 SNPs, 1767 multiple nucleotide polymorphisms, 6340 insertions, and 9137 deletions were identified. This study provides independent whole-genome resources for intra- and intersubspecies comparisons and functional genomics studies in O. sativa. Both the comparative physical maps and the GBrowse, which integrated the QTL and molecular markers from GRAMENE (http://www.gramene.org) with our physical maps and analysis results, are open to the public through our Web site (http://gresource.hzau.edu.cn/resource/resource.html).
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Damas J, Carneiro J, Amorim A, Pereira F. MitoBreak: the mitochondrial DNA breakpoints database. Nucleic Acids Res 2013; 42:D1261-8. [PMID: 24170808 PMCID: PMC3965124 DOI: 10.1093/nar/gkt982] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial DNA (mtDNA) rearrangements are key events in the development of many diseases. Investigations of mtDNA regions affected by rearrangements (i.e. breakpoints) can lead to important discoveries about rearrangement mechanisms and can offer important clues about the causes of mitochondrial diseases. Here, we present the mitochondrial DNA breakpoints database (MitoBreak; http://mitobreak.portugene.com), a free, web-accessible comprehensive list of breakpoints from three classes of somatic mtDNA rearrangements: circular deleted (deletions), circular partially duplicated (duplications) and linear mtDNAs. Currently, MitoBreak contains >1400 mtDNA rearrangements from seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Macaca mulatta, Drosophila melanogaster, Caenorhabditis elegans and Podospora anserina) and their associated phenotypic information collected from nearly 400 publications. The database allows researchers to perform multiple types of data analyses through user-friendly interfaces with full or partial datasets. It also permits the download of curated data and the submission of new mtDNA rearrangements. For each reported case, MitoBreak also documents the precise breakpoint positions, junction sequences, disease or associated symptoms and links to the related publications, providing a useful resource to study the causes and consequences of mtDNA structural alterations.
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Affiliation(s)
- Joana Damas
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Rua Dr. Roberto Frias s/n, Porto 4200-465, Portugal, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal and Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Rua dos Bragas 289, Porto 4050-123, Portugal
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Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives. Genetics 2013; 195:723-37. [PMID: 24037269 DOI: 10.1534/genetics.113.157115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.
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Kang LF, Zhu ZL, Zhao Q, Chen LY, Zhang Z. Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles. BMC Evol Biol 2012; 12:128. [PMID: 22839428 PMCID: PMC3565874 DOI: 10.1186/1471-2148-12-128] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 07/19/2012] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Retrogenes generally do not contain introns. However, in some instances, retrogenes may recruit internal exonic sequences as introns, which is known as intronization. A retrogene that undergoes intronization is a good model with which to investigate the origin of introns. Nevertheless, previously, only two cases in vertebrates have been reported. RESULTS In this study, we systematically screened the human (Homo sapiens) genome for retrogenes that evolved introns and analyzed their patterns in structure, expression and origin. In total, we identified nine intron-containing retrogenes. Alignment of pairs of retrogenes and their parents indicated that, in addition to intronization (five cases), retrogenes also may have gained introns by insertion of external sequences into the genes (one case) or reversal of the orientation of transcription (three cases). Interestingly, many intronizations were promoted not by base substitutions but by cryptic splice sites, which were silent in the parental genes but active in the retrogenes. We also observed that the majority of introns generated by intronization did not involve frameshifts. CONCLUSIONS Intron gains in retrogenes are not as rare as previously thought. Furthermore, diverse mechanisms may lead to intron creation in retrogenes. The activation of cryptic splice sites in the intronization of retrogenes may be triggered by the change of gene structure after retroposition. A high percentage of non-frameshift introns in retrogenes may be because non-frameshift introns do not dramatically affect host proteins. Introns generated by intronization in human retrogenes are generally young, which is consistent with previous findings for Caenorhabditis elegans. Our results provide novel insights into the evolutionary role of introns.
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Affiliation(s)
- Li-Fang Kang
- College of Life Sciences, Chongqing University, Chongqing 400044, China
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