99951
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Naeem A, Elbakkouri K, Alfaiz A, Hamed ME, Alsaran H, AlOtaiby S, Enani M, Alosaimi B. Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. J Med Virol 2020; 92:3016-3027. [PMID: 32159230 PMCID: PMC7228267 DOI: 10.1002/jmv.25759] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/04/2020] [Indexed: 01/19/2023]
Abstract
Antigenic drift of the hemagglutinin (HA) and neuraminidase (NA) proteins of the influenza virus cause a decrease in vaccine efficacy. Since the information about the evolution of these viruses in Saudi is deficient so we investigated the genetic diversity of circulating H1N1 viruses. Nasopharyngeal aspirates/swabs collected from 149 patients hospitalized with flu-like symptoms during 2014 and 2015 were analyzed. Viral RNA extraction was followed by a reverse transcription-polymerase chain reaction and genetic sequencing. We analyzed complete gene sequences of HA and NA from 80 positive isolates. Phylogenetic analysis of HA and NA genes of 80 isolates showed similar topologies and co-circulation of clades 6b. Genetic diversity was observed among circulating viruses belonging to clade 6B.1A. The amino acid residues in the HA epitope domain were under purifying selection. Amino acid changes at key antigenic sites, such as position S101N, S179N (antigenic site-Sa), I233T (antigenic site-Sb) in the head domain might have resulted in antigenic drift and emergence of variant viruses. For NA protein, 36% isolates showed the presence of amino acid changes such as V13I (n = 29), I314M (n = 29) and 12% had I34V (n = 10). However, H257Y mutation responsible for resistance to neuraminidase inhibitors was missing. The presence of amino acid changes at key antigenic sites and their topologies with structural mapping of residues under purifying selection highlights the importance of antigenic drift and warrants further characterization of recently circulating viruses in view of vaccine effectiveness. The co-circulation of several clades and the predominance of clade 6B.1 suggest multiple introductions in Saudi.
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Affiliation(s)
- Asif Naeem
- Research CenterKing Fahad Medical CityRiyadhSaudi Arabia
| | | | - Ali Alfaiz
- Research CenterKing Fahad Medical CityRiyadhSaudi Arabia
| | | | - Hadel Alsaran
- Research CenterKing Fahad Medical CityRiyadhSaudi Arabia
| | | | - Mushira Enani
- Medical Specialties Department, Section of Infectious DiseasesKing Fahad Medical CityRiyadhSaudi Arabia
| | - Bandar Alosaimi
- Research CenterKing Fahad Medical CityRiyadhSaudi Arabia
- College of MedicineKing Fahad Medical CityRiyadhSaudi Arabia
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99952
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Abstract
At the end of the last century, genetic studies reported that genetic information is not transmitted solely by DNA, but is also transmitted by other mechanisms, named as epigenetics. The well-described epigenetic mechanisms include DNA methylation, biochemical modifications of histones, and microRNAs. The role of altered epigenetics in the biology of various fibrotic diseases is well-established, and recent advances demonstrate its importance in the pathogenesis of pulmonary fibrosis-predominantly referring to idiopathic pulmonary fibrosis, the most lethal of the interstitial lung diseases. The deficiency in effective medications suggests an urgent need to better understand the underlying pathobiology. This review summarizes the current knowledge concerning epigenetic changes in pulmonary fibrosis and associations of these changes with several cellular pathways of known significance in its pathogenesis. It also designates the most promising substances for further research that may bring us closer to new therapeutic options.
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Affiliation(s)
- Krystian Bartczak
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland.
| | - Adam J Białas
- Department of Pathobiology of Respiratory Diseases, The Medical University of Lodz, Lodz, Poland
| | - Mateusz J Kotecki
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland
| | - Paweł Górski
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland
| | - Wojciech J Piotrowski
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland
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99953
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Chen CC, Peng CC, Fan PC, Chu PH, Chang YS, Chang CH. Practical Procedures for Improving Detection of Circulating miRNAs in Cardiovascular Diseases. J Cardiovasc Transl Res 2020; 13:977-987. [PMID: 32440912 DOI: 10.1007/s12265-020-10019-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/28/2020] [Indexed: 10/24/2022]
Abstract
Hemolysis has been known to affect the measurement of circulating biomarkers. In this study, clinically applicable procedures for microRNA (miRNA) detection in serum samples of acute myocardial infarction patients were established. The 89 samples from patients admitted to the coronary care unit were collected. These samples obtained from heparin-treated and untreated patients were subjected to heparinase digestion prior to miRNA measurements by multiplex RT-qPCR. The good reproducibility of miRNA detection after heparinase digestion (average R2 = 0.97) indicated that this method can be used routinely for samples regardless of heparin medication. Additionally, the degree of hemolysis in these samples was highly related to the hemoglobin absorbance at 414 nm. Based on the hemoglobin absorbance, five hemolysis-associated miRNAs were identified in our data normalized with respect to both the spike-in control and the RNA amount in a given sample. Using these calibration procedures, miRNAs can be accurately quantified and identified for clinical samples. Graphical Abstract The practical procedures for miRNA detection in serum samples from the coronary care unit were established, and five hemolysis-associated miRNAs were accurately clarified through serial normalization.
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Affiliation(s)
- Chia-Chun Chen
- Molecular Medicine Research Center, Chang Gung University, No. 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 33302, Taiwan.
- Department of Colorectal Surgery, Chang Gung Memorial Hospital at Linkou, No. 5 Fusing Street, Guishan District, Taoyuan City, 333, Taiwan.
| | - Chen-Ching Peng
- Molecular Medicine Research Center, Chang Gung University, No. 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 33302, Taiwan
| | - Pei-Chun Fan
- Department of Nephrology, Kidney Research Center, Chang Gung Memorial Hospital, Linkou Medical Center, College of Medicine, Chang Gung University, No. 5 Fusing Street, Guishan District, Taoyuan City, 333, Taiwan
- Graduate Institute of Clinical Medical Sciences, Chang Gung University, No. 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 33302, Taiwan
| | - Pao-Hsien Chu
- Department of Cardiology, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, 199 Tung Hwa North Road, Taipei, 105, Taiwan
| | - Yu-Sun Chang
- Molecular Medicine Research Center, Chang Gung University, No. 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 33302, Taiwan
- Graduate Institute of Biomedical Sciences, Chang Gung University, No. 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 33302, Taiwan
| | - Chih-Hsiang Chang
- Department of Nephrology, Kidney Research Center, Chang Gung Memorial Hospital, Linkou Medical Center, College of Medicine, Chang Gung University, No. 5 Fusing Street, Guishan District, Taoyuan City, 333, Taiwan
- Graduate Institute of Clinical Medical Sciences, Chang Gung University, No. 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 33302, Taiwan
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99954
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Ko JH, Son MY, Zhou Q, Molnarova L, Song L, Mlcouskova J, Jekabsons A, Montagna C, Krejci L, Hasty P. TREX2 Exonuclease Causes Spontaneous Mutations and Stress-Induced Replication Fork Defects in Cells Expressing RAD51 K133A. Cell Rep 2020; 33:108543. [PMID: 33357432 DOI: 10.1016/j.celrep.2020.108543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 04/23/2020] [Accepted: 12/01/2020] [Indexed: 01/01/2023] Open
Abstract
DNA damage tolerance (DDT) and homologous recombination (HR) stabilize replication forks (RFs). RAD18/UBC13/three prime repair exonuclease 2 (TREX2)-mediated proliferating cell nuclear antigen (PCNA) ubiquitination is central to DDT, an error-prone lesion bypass pathway. RAD51 is the recombinase for HR. The RAD51 K133A mutation increased spontaneous mutations and stress-induced RF stalls and nascent strand degradation. Here, we report in RAD51K133A cells that this phenotype is reduced by expressing a TREX2 H188A mutation that deletes its exonuclease activity. In RAD51K133A cells, knocking out RAD18 or overexpressing PCNA reduces spontaneous mutations, while expressing ubiquitination-incompetent PCNAK164R increases mutations, indicating DDT as causal. Deleting TREX2 in cells deficient for the RF maintenance proteins poly(ADP-ribose) polymerase 1 (PARP1) or FANCB increased nascent strand degradation that was rescued by TREX2H188A, implying that TREX2 prohibits degradation independent of catalytic activity. A possible explanation for this occurrence is that TREX2H188A associates with UBC13 and ubiquitinates PCNA, suggesting a dual role for TREX2 in RF maintenance.
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99955
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Cui L, Fan M, Belanger S, Li J, Wang X, Fan B, Li W, Gao X, Chen J, Liu Z. Oryzias sinensis, a new model organism in the application of eco-toxicity and water quality criteria (WQC). Chemosphere 2020; 261:127813. [PMID: 32768750 DOI: 10.1016/j.chemosphere.2020.127813] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 06/11/2023]
Abstract
Fish play an important role as a primary eco-toxicity test organism in environmental hazard assessment. Toxicity data of native species are often sought for use in the derivation of water quality criteria (WQC). The Chinese medaka, Oryzias sinensis, is an endemic species of China. The acute toxicity of 6 chemicals on O. sinensis was tested in this work, and toxicity effect of 10 chemicals to O. sinensis was compared with 4 commonly used species globally. A total of 9 robust interspecies correlation estimation (ICE) models using O. sinensis as the surrogate species were constructed and used to derive predicted no effect concentration and hazardous concentrations of 5% species (HC5) values based on species sensitivity distribution. Results showed that the 96 h median lethal concentration of Hg2+, Cr6+, linear alkylbenzene sulfonates, triclosan, 3,4-dchloroaniline, sodium chloride to O. sinensis were 0.29, 50, 6.0, 0.63, 9.2 and 14,400 mg/L, respectively. The sensitivity of O. sinensis and other 4 testing organisms were statistically indistinguishable (P > 0.05). No significant difference among HC5-ICE, HC5-measured and HC5 from published literatures was identified. All results indicated the O. sinensis is a potential model organism in the application of eco-toxicity and WQC in China and other Asian countries.
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Affiliation(s)
- Liang Cui
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Ming Fan
- Global Product Stewardship, The Procter and Gamble Company, 8700 Mason Montgomery Road, Mason, OH, 45040, United States
| | - Scott Belanger
- Global Product Stewardship, The Procter and Gamble Company, 8700 Mason Montgomery Road, Mason, OH, 45040, United States
| | - Ji Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xiaonan Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Bo Fan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Wenwen Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Environmental and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Xiangyun Gao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Jin Chen
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Zhengtao Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
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99956
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Cepon-Robins TJ. Measuring attack on self: The need for field-friendly methods development and research on autoimmunity in human biology. Am J Hum Biol 2020; 33. [PMID: 33289250 DOI: 10.1002/ajhb.23544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Autoimmune and inflammatory disorder (AIID) prevalence appears to be increasing in all but the world's poorest regions and countries. Autoimmune diseases occur when there is a breakdown in processes that regulate inflammation and self-recognition by immune cells. Very few field-based studies have been conducted among Indigenous populations and underserved communities with limited access to medical care. This is due, in part, to the fact that autoimmune diseases are difficult to diagnose, even in clinical settings. In remote field settings these difficulties are compounded by the absence of infrastructure necessary for sample storage and analysis, and the lack of hospital/clinic access for more invasive diagnostic procedures. Because of these limitations, little is known about the prevalence of autoimmunity outside wealthy regions and clinical settings. AIMS The present paper discusses why AIID are of critical importance in human biology research and why more work needs to be devoted to validating, testing, and utilizing methods for detecting autoantibodies and other biomarkers related to autoimmunity in field-friendly, minimally invasively-collected samples. This paper reviews some of the methods used to diagnose AIIDs in clinical settings, and highlights methods that have been used in studies within human biology and related fields, emphasizing the invasiveness of specific methods and their feasibility in remote field settings. DISCUSSION AND CONCLUSIONS Risk for AIID is affected by several reproductive, dietary, environmental, and genetic factors. Human biologists have unique perspectives that they can bring to autoimmunity research, and more population-based studies on autoimmunity are needed within these and related fields.
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Affiliation(s)
- Tara J Cepon-Robins
- Department of Anthropology, University of Colorado Colorado Springs, Colorado Springs, Colorado, USA
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99957
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Napoli C, Benincasa G, Schiano C, Salvatore M. Differential epigenetic factors in the prediction of cardiovascular risk in diabetic patients. European Heart Journal - Cardiovascular Pharmacotherapy 2020; 6:239-247. [PMID: 31665258 PMCID: PMC7363021 DOI: 10.1093/ehjcvp/pvz062] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/02/2019] [Accepted: 10/24/2019] [Indexed: 12/30/2022]
Abstract
Hyperglycaemia can strongly alter the epigenetic signatures in many types of human vascular cells providing persistent perturbations of protein–protein interactions both in micro- and macro-domains. The establishment of these epigenetic changes may precede cardiovascular (CV) complications and help us to predict vascular lesions in diabetic patients. Importantly, these epigenetic marks may be transmitted across several generations (transgenerational effect) and increase the individual risk of disease. Aberrant DNA methylation and imbalance of histone modifications, mainly acetylation and methylation of H3, represent key determinants of vascular lesions and, thus, putative useful biomarkers for prevention and diagnosis of CV risk in diabetics. Moreover, a differential expression of some micro-RNAs (miRNAs), mainly miR-126, may be a useful prognostic biomarker for atherosclerosis development in asymptomatic subjects. Recently, also environmental-induced chemical perturbations in mRNA (epitranscriptome), mainly the N6-methyladenosine, have been associated with obesity and diabetes. Importantly, reversal of epigenetic changes by modulation of lifestyle and use of metformin, statins, fenofibrate, and apabetalone may offer useful therapeutic options to prevent or delay CV events in diabetics increasing the opportunity for personalized therapy. Network medicine is a promising molecular-bioinformatic approach to identify the signalling pathways underlying the pathogenesis of CV lesions in diabetic patients. Moreover, machine learning tools combined with tomography are advancing the individualized assessment of CV risk in these patients. We remark the need for combining epigenetics and advanced bioinformatic platforms to improve the prediction of vascular lesions in diabetics increasing the opportunity for CV precision medicine.
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Affiliation(s)
- Claudio Napoli
- Department of Advanced Clinical and Surgical Sciences, University of Campania "Luigi Vanvitelli", Pz. Miraglia 2, Naples 80138, Italy.,IRCCS SDN, via E. Gianturco 113, Naples 80143, Italy
| | - Giuditta Benincasa
- Department of Advanced Clinical and Surgical Sciences, University of Campania "Luigi Vanvitelli", Pz. Miraglia 2, Naples 80138, Italy
| | - Concetta Schiano
- Department of Advanced Clinical and Surgical Sciences, University of Campania "Luigi Vanvitelli", Pz. Miraglia 2, Naples 80138, Italy
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99958
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Miyazaki T, Oba N, Park EY. Structural insight into the substrate specificity of Bombyx mori β-fructofuranosidase belonging to the glycoside hydrolase family 32. Insect Biochem Mol Biol 2020; 127:103494. [PMID: 33132139 DOI: 10.1016/j.ibmb.2020.103494] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
Sucrose-hydrolyzing enzymes are largely divided into β-fructofuranosidase and sucrose α-glucosidase. The domestic silkworm Bombyx mori possesses both enzymes, BmSUC1 and BmSUH, belonging to the glycoside hydrolase family 32 (GH32) and GH13, respectively. BmSUC1 was presumed to be acquired by horizontal gene transfer from bacteria based on phylogenetic analysis and related to tolerance to sugar-mimic alkaloids contained in mulberry latex. Here we investigated the substrate specificity of recombinant BmSUC1 that can hydrolyze not only sucrose but also fructooligosaccharides and fructans, and revealed that the enzyme was competitively inhibited by 1,4-dideoxy-1,4-imino-D-arabinitol, one of the alkaloids. Moreover, the crystal structures of BmSUC1 in apo form and complex with sucrose were determined, and the active site pocket was shallow and suitable for shorter substrates but was related to more relaxed substrate specificity than the strict sucrose α-glucosidase BmSUH. Considering together with the distribution of BmSUC1-orthologous genes in many lepidopterans, our results suggest that BmSUC1 contributes to the digestion of fructooligosaccharides and fructans derived from feed plants.
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Affiliation(s)
- Takatsugu Miyazaki
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
| | - Nozomi Oba
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Enoch Y Park
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
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99959
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Hop PJ, Zwamborn RAJ, Hannon EJ, Dekker AM, van Eijk K, Walker E, Iacoangeli A, Jones A, Shatunov A, Khleifat AA, Opie-Martin S, Shaw C, Morrison K, Shaw P, McLaughlin R, Hardiman O, Al-Chalabi A, Van Den Berg L, Mill J, Veldink JH. Cross-reactive probes on Illumina DNA methylation arrays: a large study on ALS shows that a cautionary approach is warranted in interpreting epigenome-wide association studies. NAR Genom Bioinform 2020; 2:lqaa105. [PMID: 33554115 PMCID: PMC7745769 DOI: 10.1093/nargab/lqaa105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/27/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022] Open
Abstract
Illumina DNA methylation arrays are a widely used tool for performing genome-wide DNA methylation analyses. However, measurements obtained from these arrays may be affected by technical artefacts that result in spurious associations if left unchecked. Cross-reactivity represents one of the major challenges, meaning that probes may map to multiple regions in the genome. Although several studies have reported on this issue, few studies have empirically examined the impact of cross-reactivity in an epigenome-wide association study (EWAS). In this paper, we report on cross-reactivity issues that we discovered in a large EWAS on the presence of the C9orf72 repeat expansion in ALS patients. Specifically, we found that that the majority of the significant probes inadvertently cross-hybridized to the C9orf72 locus. Importantly, these probes were not flagged as cross-reactive in previous studies, leading to novel insights into the extent to which cross-reactivity can impact EWAS. Our findings are particularly relevant for epigenetic studies into diseases associated with repeat expansions and other types of structural variation. More generally however, considering that most spurious associations were not excluded based on pre-defined sets of cross-reactive probes, we believe that the presented data-driven flag and consider approach is relevant for any type of EWAS.
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Affiliation(s)
- Paul J Hop
- Department of Neurology, UMC Utrecht Brain Center, 3584 CG, Utrecht, the Netherlands
| | - Ramona A J Zwamborn
- Department of Neurology, UMC Utrecht Brain Center, 3584 CG, Utrecht, the Netherlands
| | - Eilis J Hannon
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Annelot M Dekker
- Department of Neurology, UMC Utrecht Brain Center, 3584 CG, Utrecht, the Netherlands
| | - Kristel R van Eijk
- Department of Neurology, UMC Utrecht Brain Center, 3584 CG, Utrecht, the Netherlands
| | - Emma M Walker
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RS, UK
- Department of Biostatistics and Health Informatics, King’s College London, London SE5 8AF, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RS, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RS, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RS, UK
| | - Sarah Opie-Martin
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RS, UK
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RS, UK
- UK Dementia Research Institute, King’s College London, London WC2R 2LS, UK
| | - Karen E Morrison
- Faculty of Medicine, Health & Life Sciences, Queen’s University Belfast, 90 Lisburn Road, Belfast, BT9 6AG, Northern Ireland, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Russell L McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 DK07, Republic of Ireland
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin D02 PN40, Republic of Ireland
- Department of Neurology, Beaumont Hospital, Dublin D02 PN40, Republic of Ireland
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RS, UK
- Department of Neurology, King’s College Hospital, Bessemer Road, London, SE5 9RX, UK
| | | | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Jan H Veldink
- Department of Neurology, UMC Utrecht Brain Center, 3584 CG, Utrecht, the Netherlands
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99960
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Hua X, Zhang L, Moran RA, Xu Q, Sun L, van Schaik W, Yu Y. Cointegration as a mechanism for the evolution of a KPC-producing multidrug resistance plasmid in Proteus mirabilis. Emerg Microbes Infect 2020; 9:1206-1218. [PMID: 32438864 PMCID: PMC7448864 DOI: 10.1080/22221751.2020.1773322] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/19/2020] [Indexed: 11/26/2022]
Abstract
The incidence and transmission of Klebsiella pneumoniae carbapenemase (KPC) producing plasmids have been well documented. However, the evolutionary dynamics of KPC plasmids and their fitness costs are not well characterized. Here, two carbapenemase-producing plasmids from Proteus mirabilis, pT18 and pT211 (both carrying bla KPC-2), were characterized through whole genome sequencing. pT211 is a 24.2 kbp N-type plasmid that contains bla KPC-2 and a single copy of the IS6-family insertion sequence IS26. pT18 is a 59 kbp cointegrate plasmid comprised of sequences derived from three different plasmids: a close relative of pT211 (containing bla KPC-2), an FII-33 plasmid (bla TEM-1B, bla CTX-M-65, rmtB and fosA3) and a rolling-circle plasmid. The segments of pT18 derived from each of the different plasmids are separated by copies of IS26, and sequence analysis indicated that pT18 was likely generated by both conservative and replicative IS26-mediated cointegrate formation. pT18 and pT211 were transferred into Escherichia coli DH5α separately to assess the impact of plasmids on host fitness. Only DH5α harbouring pT18 grew slower than the wild type in antibiotic-free media. However, in sub-inhibitory concentrations of fosfomycin and amikacin, cells containing pT18 grew faster than the wild type, and the minimum concentrations of fosfomycin and amikacin required to observe an advantage for plasmid-carrying cells were 1/3 and 1/20 the DH5α MIC, respectively. This study highlights the importance of the role of cointegrate plasmids in the dissemination of antibiotic resistance genes between pathogenic bacterial species, and highlights the importance of sub-inhibitory concentrations of antibiotics to the persistence of such plasmids.
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Affiliation(s)
- Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
| | - Linyue Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
| | - Robert A. Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, The University of Birmingham, Birmingham, United Kingdom
| | - Qingye Xu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
| | - Long Sun
- Department of Clinical Laboratory, Hangzhou Women’ s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, People’s Republic of China
- Department of Clinical Laboratory, Hangzhou Hospital of Zhejiang Provincial Corps, Chinese People’s Armed Police Forces, Hangzhou, People’s Republic of China
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, The University of Birmingham, Birmingham, United Kingdom
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
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99961
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Alexandri C, Daniel A, Bruylants G, Demeestere I. The role of microRNAs in ovarian function and the transition toward novel therapeutic strategies in fertility preservation: from bench to future clinical application. Hum Reprod Update 2020; 26:174-196. [PMID: 32074269 DOI: 10.1093/humupd/dmz039] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/02/2019] [Accepted: 10/01/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND New therapeutic approaches in oncology have converted cancer from a certain death sentence to a chronic disease. However, there are still challenges to be overcome regarding the off-target toxicity of many of these treatments. Oncological therapies can lead to future infertility in women. Given this negative impact on long-term quality of life, fertility preservation is highly recommended. While gamete and ovarian tissue cryopreservation are the usual methods offered, new pharmacological-based options aiming to reduce ovarian damage during oncological treatment are very attractive. In this vein, advances in the field of transcriptomics and epigenomics have brought small noncoding RNAs, called microRNAs (miRNAs), into the spotlight in oncology. MicroRNAs also play a key role in follicle development as regulators of follicular growth, atresia and steroidogenesis. They are also involved in DNA damage repair responses and they can themselves be modulated during chemotherapy. For these reasons, miRNAs may be an interesting target to develop new protective therapies during oncological treatment. This review summarizes the physiological role of miRNAs in reproduction. Considering recently developed strategies based on miRNA therapy in oncology, we highlight their potential interest as a target in fertility preservation and propose future strategies to make the transition from bench to clinic. OBJECTIVE AND RATIONALE How can miRNA therapeutic approaches be used to develop new adjuvant protective therapies to reduce the ovarian damage caused by cytotoxic oncological treatments? SEARCH METHODS A systematic search of English language literature using PubMed and Google Scholar databases was performed through to 2019 describing the role of miRNAs in the ovary and their use for diagnosis and targeted therapy in oncology. Personal data illustrate miRNA therapeutic strategies to target the gonads and reduce chemotherapy-induced follicular damage. OUTCOMES This review outlines the importance of miRNAs as gene regulators and emphasizes the fact that insights in oncology can inspire new adjuvant strategies in the field of onco-fertility. Recent improvements in nanotechnology offer the opportunity for drug development using next-generation miRNA-nanocarriers. WIDER IMPLICATIONS Although there are still some barriers regarding the immunogenicity and toxicity of these treatments and there is still room for improvement concerning the specific delivery of miRNAs into the ovaries, we believe that, in the future, miRNAs can be developed as powerful and non-invasive tools for fertility preservation.
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Affiliation(s)
- C Alexandri
- Research Laboratory in Human Reproduction, Faculty of Medicine, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - A Daniel
- Research Laboratory in Human Reproduction, Faculty of Medicine, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium.,Université de Tours, Faculty of Science and Technology, 37200 Tours, France
| | - G Bruylants
- Engineering of Molecular NanoSystems, Ecole Polytechnique de Bruxelles, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - I Demeestere
- Research Laboratory in Human Reproduction, Faculty of Medicine, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium.,Fertility Clinic, CUB-Erasme, 1070 Brussels, Belgium
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99962
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Zhu S, Chen J, Zhao J, Comes HP, Li P, Fu C, Xie X, Lu R, Xu W, Feng Y, Ye W, Sakaguchi S, Isagi Y, Li L, Lascoux M, Qiu Y. Genomic insights on the contribution of balancing selection and local adaptation to the long-term survival of a widespread living fossil tree, Cercidiphyllum japonicum. New Phytol 2020; 228:1674-1689. [PMID: 32643803 DOI: 10.1111/nph.16798] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/27/2020] [Indexed: 05/25/2023]
Abstract
'Living fossils' are testimonies of long-term sustained ecological success, but how demographic history and natural selection contributed to their survival, resilience, and persistence in the face of Quaternary climate fluctuations remains unclear. To better understand the interplay between demographic history and selection in shaping genomic diversity and evolution of such organisms, we assembled the whole genome of Cercidiphyllum japonicum, a widespread East Asian Tertiary relict tree, and resequenced 99 individuals of C. japonicum and its sister species, Cercidiphyllum magnificum (Central Japan). We dated this speciation event to the mid-Miocene, and the intraspecific lineage divergence of C. japonicum (China vs Japan) to the Early Pliocene. Throughout climatic upheavals of the late Tertiary/Quaternary, population bottlenecks greatly reduced the genetic diversity of C. japonicum. However, this polymorphism loss was likely counteracted by, first, long-term balancing selection at multiple chromosomal and heterozygous gene regions, potentially reflecting overdominance, and, second, selective sweeps at stress response and growth-related genes likely involved in local adaptation. Our findings contribute to a better understanding of how living fossils have survived climatic upheaval and maintained an extensive geographic range; that is, both types of selection could be major factors contributing to the species' survival, resilience, and persistence.
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Affiliation(s)
- Shanshan Zhu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jing Zhao
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Hans Peter Comes
- Department of Biosciences, Salzburg University, Salzburg, A-5020, Austria
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Chengxin Fu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xiao Xie
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Ruisen Lu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wuqin Xu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yu Feng
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wenqing Ye
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Yingxiong Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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99963
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Onishi R, Sato K, Murano K, Negishi L, Siomi H, Siomi MC. Piwi suppresses transcription of Brahma-dependent transposons via Maelstrom in ovarian somatic cells. Sci Adv 2020; 6:6/50/eaaz7420. [PMID: 33310860 PMCID: PMC7732180 DOI: 10.1126/sciadv.aaz7420] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 10/19/2020] [Indexed: 05/05/2023]
Abstract
Drosophila Piwi associates with PIWI-interacting RNAs (piRNAs) and represses transposons transcriptionally through heterochromatinization; however, this process is poorly understood. Here, we identify Brahma (Brm), the core adenosine triphosphatase of the SWI/SNF chromatin remodeling complex, as a new Piwi interactor, and show Brm involvement in activating transcription of Piwi-targeted transposons before silencing. Bioinformatic analyses indicated that Piwi, once bound to target RNAs, reduced the occupancies of SWI/SNF and RNA polymerase II (Pol II) on target loci, abrogating transcription. Artificial piRNA-driven targeting of Piwi to RNA transcripts enhanced repression of Brm-dependent reporters compared with Brm-independent reporters. This was dependent on Piwi cofactors, Gtsf1/Asterix (Gtsf1), Panoramix/Silencio (Panx), and Maelstrom (Mael), but not Eggless/dSetdb (Egg)-mediated H3K9me3 deposition. The λN-box B-mediated tethering of Mael to reporters repressed Brm-dependent genes in the absence of Piwi, Panx, and Gtsf1. We propose that Piwi, via Mael, can rapidly suppress transcription of Brm-dependent genes to facilitate heterochromatin formation.
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Affiliation(s)
- Ryo Onishi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Kaoru Sato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Kensaku Murano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Lumi Negishi
- Central Laboratory, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan.
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99964
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Fang Y, Park MG, Choi JY, Park DH, Wang M, Kim HJ, Kim WJ, Je YH. Insecticidal and synergistic activity of dsRNAs targeting buprofezin-specific genes against the small brown planthopper, Laodelphax striatellus. Arch Insect Biochem Physiol 2020; 105:e21739. [PMID: 32929790 DOI: 10.1002/arch.21739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/12/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
The small brown planthopper, Laodelphax striatellus, is a dangerous pest in rice fields. Although buprofezin has been used to control L. striatellus for more than a decade, the occurrence of buprofezin-resistant L. striatellus has been recently reported. To develop an alternative pest control strategy, comparative transcriptome analysis of buprofezin-treated and nontreated L. striatellus was performed to screen the buprofezin-specific target genes for RNA interference (RNAi) application. Among six genes downregulated in the buprofezin-treated L. striatellus, RNAi-based silencing of the lipophorin precursor, endocuticle structure glycoprotein, and chitin synthase significantly induced the lethality of L. striatellus in a concentration-dependent manner. In addition, a cocktail of double-stranded RNAs against these three genes showed synergistic effects with buprofezin. These results provide RNAi-based effective approaches to control L. striatellus as well as an efficient method to identify novel target genes for RNAi application.
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Affiliation(s)
- Ying Fang
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Min G Park
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jae Y Choi
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dong H Park
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Minghui Wang
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyun J Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Woo J Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yeon H Je
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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99965
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Alaizari NA, Al-Anazi JR. Oral Candida carriage in smokers and tobacco users: A systematic review and meta-analysis of observational studies. J Oral Biosci 2020; 62:342-348. [PMID: 33038515 DOI: 10.1016/j.job.2020.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To synthesize evidence from observational studies that evaluated the association between smoking and smokeless tobacco with oral Candida carriage. METHODS Following the PRISMA guidelines, we searched through PubMed/MEDLINE, Web of Science, Embase, and Scopus without restrictions until April 2020 for studies that assessed this association. Following study retrieval and selection, relevant data were extracted, and the risk of bias was assessed by two independent authors using the Newcastle-Ottawa Scale. A fixed-effect meta-analysis was performed due to insignificant heterogeneity between studies. RESULTS We identified 14 studies that were eligible for inclusion in this review. The pooled odds ratio (OR; six studies) for Candida carriage among smokers and non-smokers was 2.15 (95% confidence interval [CI]: 1.47, 3.14; I2 = 8%; P < 0.0001). The OR (five studies) for Candida carriage among smokeless tobacco users and non-users was 1.77 (95% CI: 1.29, 2.44; I2 = 46%; P = 0.0004). CONCLUSION Our findings suggest a significant relationship between smoking/smokeless tobacco users and oral Candida carriage. However, observational studies cannot clarify whether the observed epidemiologic association is a causal effect or the result of some unmeasured confounding variables. Therefore, continued efforts to measure the association between smoking and oral Candida carriage are required.
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Affiliation(s)
- Nader A Alaizari
- Department of Oral Medicine and Diagnostic Sciences, AlFarabi College of Dentistry and Nursing, Riyadh, Saudi Arabia.
| | - Jamilah R Al-Anazi
- Department of Oral Medicine and Diagnostic Sciences, AlFarabi College of Dentistry and Nursing, Riyadh, Saudi Arabia.
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99966
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Ranawaka B, Tanurdzic M, Waterhouse P, Naim F. An optimised chromatin immunoprecipitation (ChIP) method for starchy leaves of Nicotiana benthamiana to study histone modifications of an allotetraploid plant. Mol Biol Rep 2020; 47:9499-9509. [PMID: 33237398 PMCID: PMC7723940 DOI: 10.1007/s11033-020-06013-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/16/2020] [Indexed: 10/26/2022]
Abstract
All flowering plants have evolved through multiple rounds of polyploidy throughout the evolutionary process. Intergenomic interactions between subgenomes in polyploid plants are predicted to induce chromatin modifications such as histone modifications to regulate expression of gene homoeologs. Nicotiana benthamiana is an ancient allotetraploid plant with ecotypes collected from climatically diverse regions of Australia. Studying the chromatin landscape of this unique collection will likely shed light on the importance of chromatin modifications in gene regulation in polyploids as well its implications in adaptation of plants in environmentally diverse conditions. Generally, chromatin immunoprecipitation and high throughput DNA sequencing (ChIP-seq) is used to study chromatin modifications. However, due to the starchy nature of mature N. benthamiana leaves, previously published protocols were unsuitable. The higher amounts of starch in leaves that co-precipitated with nuclei hindered downstream processing of DNA. Here we present an optimised ChIP protocol for N. benthamiana leaves to facilitate comparison of chromatin modifications in two closely related ecotypes. Several steps of ChIP were optimised including tissue harvesting, nuclei isolation, nuclei storage, DNA shearing and DNA recovery. Commonly available antibodies targeting histone 3 lysine 4 trimethylation (H3K4me3) and histone 3 lysine 9 dimethylation (H3K9me2) histone modifications were used and success of ChIP was confirmed by PCR and next generation sequencing. Collectively, our optimised method is the first comprehensive ChIP method for mature starchy leaves of N. benthamiana to enable studies of chromatin landscape at the genome-wide scale.
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Affiliation(s)
- Buddhini Ranawaka
- Centre for Agriculture and Bioeconomy, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
| | - Milos Tanurdzic
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Peter Waterhouse
- Centre for Agriculture and Bioeconomy, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Fatima Naim
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
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99967
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Yang J, Li L, Hong S, Zhang D, Zhou Y. Methamphetamine leads to the alterations of microRNA profiles in the nucleus accumbens of rats. Pharm Biol 2020; 58:797-805. [PMID: 32893733 PMCID: PMC8641683 DOI: 10.1080/13880209.2020.1803366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 07/07/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
CONTEXT MicroRNA (miRNA) is an important regulator of gene expression. Methamphetamine (METH) induces a variety of alterations in different systems by affecting gene expression, but the effects of METH on miRNA profiles need to be elucidated. OBJECTIVES This study develops a rat model of METH addiction, and analyzes the expression profile alterations of miRNA in nucleus accumbens (NAc) of the METH-addicted rats. MATERIALS AND METHODS Sprague-Dawley rats were administered 10 mg/kg METH or vehicle twice a day for 4 weeks. The addictive behaviour of rats was estimated by CPP test. The pathological changes of brain tissues were then observed by HE and Glee silver staining. The miRNA profile analysis of the NAc of the rats was performed using an Illumina HiSeq™ 2500 sequencing system. RESULTS CPP test indicated that METH significantly prolonged the residence time of the rats in the drug box (from 307 ± 97 to 592 ± 96 s). The pathological staining showed the distorted axons, and fewer polarized neurons in the METH-treated rats. We further identified 40 differential miRNAs (17 up- and 23 down-regulated) and three novel miRNAs (novel 237, 296 and 501) that responded to METH. The bioinformatic analysis for the potential targets of the differential miRNA suggests that the downstream were concentrated in the Wnt signalling pathway, tuberculosis, toxoplasmosis, spliceosome, lysosome, and axon guidance. DISCUSSION AND CONCLUSIONS A number of miRNAs responding to METH were identified in the NAc of rats. These METH-regulated miRNAs provide a new perspective for revealing the molecular mechanisms of METH addiction.
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Affiliation(s)
- Jing Yang
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan, China
| | - Lihua Li
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan, China
| | - Shijun Hong
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan, China
| | - Dongxian Zhang
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan, China
| | - Yiqing Zhou
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan, China
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99968
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Siqueiros Sanchez M, Falck‐Ytter T, Kennedy DP, Bölte S, Lichtenstein P, D'Onofrio BM, Pettersson E. Volitional eye movement control and ADHD traits: a twin study. J Child Psychol Psychiatry 2020; 61:1309-1316. [PMID: 32020616 PMCID: PMC7754462 DOI: 10.1111/jcpp.13210] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/03/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND Top-down volitional command of eye movements may serve as a candidate endophenotype of ADHD, an important function underlying goal-directed action in everyday life. In this twin study, we examined the relation between performance on a response inhibition eye-tracking paradigm and parent-rated ADHD traits in a population-based twin sample. We hypothesized that altered eye movement control is associated with the severity of ADHD traits and that this association is attributable to genetic factors. METHODS A total of 640 twins (320 pairs, 50% monozygotic) aged 9-14 years) from the Child and Adolescent Twin Study in Sweden (CATSS) participated. Twins performed the antisaccade task indexing inhibitory alterations as either direction errors (following exogenous cues rather than instructions) or premature anticipatory eye movements (failure to wait for cues). We calculated the associations of eye movement control and ADHD traits using linear regression mixed-effects models and genetic and environmental influences with multivariate twin models. RESULTS Premature anticipatory eye movements were positively associated with inattentive traits (β = .17; 95% CI: 0.04, 0.31), while controlling for hyperactive behaviors and other covariates. Both premature anticipatory eye movements and inattention were heritable (h2 = 0.40, 95% CI: 0.22, 0.56; h2 = 0.55; 95% CI: 0.42, 0.65; respectively), and their genetic correlation was small but statistically significant (r = .19, 95% CI: 0.02, 0.36). However, the genetic correlation did not remain significant after adjusting for covariates (age, sex, hyperactivity traits, IQ). No link was found between direction errors and ADHD traits. CONCLUSIONS This study indicates that there is a specific, genetically influenced, relation between top-down eye movement control and the inattentive traits typical of ADHD.
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Affiliation(s)
- Monica Siqueiros Sanchez
- Karolinska Institutet Center of Neurodevelopmental Disorders (KIND)Department of Women’s and Children’s HealthKarolinska InstitutetStockholmSweden
| | - Terje Falck‐Ytter
- Karolinska Institutet Center of Neurodevelopmental Disorders (KIND)Department of Women’s and Children’s HealthKarolinska InstitutetStockholmSweden,Department of PsychologyUppsala UniversityUppsalaSweden,Swedish Collegium for Advanced Study (SCAS)UppsalaSweden
| | - Daniel P. Kennedy
- Department of Psychological and Brain SciencesIndiana UniversityBloomingtonINUSA
| | - Sven Bölte
- Karolinska Institutet Center of Neurodevelopmental Disorders (KIND)Department of Women’s and Children’s HealthKarolinska InstitutetStockholmSweden,Child and Adolescent PsychiatryStockholm Health Care ServicesStockholmSweden,Curtin Autism Research GroupSchool of Occupational Therapy, Social Work and Speech PathologyCurtin UniversityPerthWAAustralia
| | - Paul Lichtenstein
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Brian M. D'Onofrio
- Department of Psychological and Brain SciencesIndiana UniversityBloomingtonINUSA,Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Erik Pettersson
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
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99969
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Arauz RF, Byun JS, Tandon M, Sinha S, Kuhn S, Taylor S, Zingone A, Mitchell KA, Pine SR, Gardner K, Perez-Stable EJ, Napoles AM, Ryan BM. Whole-Exome Profiling of NSCLC Among African Americans. J Thorac Oncol 2020; 15:1880-1892. [PMID: 32931935 PMCID: PMC7704928 DOI: 10.1016/j.jtho.2020.08.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Lung cancer incidence is higher among African Americans (AAs) compared with European Americans (EAs) in the United States, especially among men. Although significant progress has been made profiling the genomic makeup of lung cancer in EAs, AAs continue to be underrepresented. Our objective was to chart the genome-wide landscape of somatic mutations in lung cancer tumors from AAs. METHODS In this study, we used the whole-exome sequencing of 82 tumor and noninvolved tissue pairs from AAs. Patients were selected from an ongoing case-control study conducted by the National Cancer Institute and the University of Maryland. RESULTS Among all samples, we identified 178 significantly mutated genes (p < 0.05), five of which passed the threshold for false discovery rate (p < 0.1). In lung adenocarcinoma (LUAD) tumors, mutation rates in STK11 (p = 0.05) and RB1 (p = 0.008) were significantly higher in AA LUAD tumors (25% and 13%, respectively) compared with The Cancer Genome Atlas EA samples (14% and 4%, respectively). In squamous cell carcinomas, mutation rates in STK11 (p = 0.002) were significantly higher among AA (8%) than EA tumors from The Cancer Genome Atlas (1%). Integrated somatic mutation data with CIBERSORT (Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts) data analysis revealed LUAD tumors from AAs carrying STK11 mutations have decreased interferon signaling. CONCLUSIONS Although a considerable degree of the somatic mutation landscape is shared between EAs and AAs, discrete differences in mutation frequency in potentially important oncogenes and tumor suppressors exist. A better understanding of the molecular basis of lung cancer in AA patients and leveraging this information to guide clinical interventions may help reduce disparities.
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Affiliation(s)
- Rony F Arauz
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Jung S Byun
- Division of Intramural Research, National Institute on Minority Health and Health Disparities, Bethesda, Maryland; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Mayank Tandon
- CCR Collaborative Bioinformatics Resource CCBR, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Sanju Sinha
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland; Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Skyler Kuhn
- CCR Collaborative Bioinformatics Resource CCBR, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Sheryse Taylor
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Adriana Zingone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Khadijah A Mitchell
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Sharon R Pine
- Departments of Pharmacology and Medicine, Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Kevin Gardner
- National Institute of Minority Health and Health Disparities, Bethesda, Maryland; Department of Pathology and Cell Biology, Columbia University Medical Center, Columbia University, New York, New York
| | | | - Anna M Napoles
- National Institute of Minority Health and Health Disparities, Bethesda, Maryland
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.
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99970
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Strzelecka D, Smietanski M, Sikorski PJ, Warminski M, Kowalska J, Jemielity J. Phosphodiester modifications in mRNA poly(A) tail prevent deadenylation without compromising protein expression. RNA 2020; 26:1815-1837. [PMID: 32820035 PMCID: PMC7668260 DOI: 10.1261/rna.077099.120] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/13/2020] [Indexed: 06/07/2023]
Abstract
Chemical modifications enable preparation of mRNAs with augmented stability and translational activity. In this study, we explored how chemical modifications of 5',3'-phosphodiester bonds in the mRNA body and poly(A) tail influence the biological properties of eukaryotic mRNA. To obtain modified and unmodified in vitro transcribed mRNAs, we used ATP and ATP analogs modified at the α-phosphate (containing either O-to-S or O-to-BH3 substitutions) and three different RNA polymerases-SP6, T7, and poly(A) polymerase. To verify the efficiency of incorporation of ATP analogs in the presence of ATP, we developed a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for quantitative assessment of modification frequency based on exhaustive degradation of the transcripts to 5'-mononucleotides. The method also estimated the average poly(A) tail lengths, thereby providing a versatile tool for establishing a structure-biological property relationship for mRNA. We found that mRNAs containing phosphorothioate groups within the poly(A) tail were substantially less susceptible to degradation by 3'-deadenylase than unmodified mRNA and were efficiently expressed in cultured cells, which makes them useful research tools and potential candidates for future development of mRNA-based therapeutics.
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Affiliation(s)
- Dominika Strzelecka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | | | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
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99971
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Bahrami G, Sajadimajd S, Mohammadi B, Hatami R, Miraghaee S, Keshavarzi S, Khazaei M, Madani SH. Anti-diabetic effect of a novel oligosaccharide isolated from Rosa canina via modulation of DNA methylation in Streptozotocin-diabetic rats. Daru 2020; 28:581-590. [PMID: 32748125 PMCID: PMC7704860 DOI: 10.1007/s40199-020-00363-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 07/28/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Diabetes mellitus (DM) is a well-known clinical entity with various late complications. There is a surge of research aiming to use the medical herb in the management of DM. OBJECTIVE This study aimed to investigate whether the alleviation of DM by an isolated compound from Rosa canina is mediated by DNA methylation in STZ-diabetic rats. METHODS Sixty adult Wistar male rats were classified into control, diabetic and treatment groups. Rats were treated with STZ (40 mg/kg), metformin (500 mg/kg), and oligosaccharide fraction (OF; 10, 20 and 30 mg/kg) isolated from Rosa canina. DNA was extracted from the blood and pancreas to determine DNA methylation using the Global DNA Methylation kit. The expressions of DNA methyltransferases (Dnmts), PDX1, Ins1, GCK and PTP1B2 were determined by using qRT-PCR. RESULTS The significant blood glucose-lowering potential of OF was associated with a reduced level of global DNA methylation (p < 0.05). The expression levels of Dnmts 1 and 3α increased in the pancreas and blood from diabetic rats compared to control group which declined by OF treatment (p < 0.05). Paradoxically, the expression of Dnmt 3β augmented in the pancreas and blood of OF group compared to diabetic ones (p < 0.05). Besides, the expressions of Pdx1, PTP1B2, Ins1 and GCK increased in OF-treated rats compared to diabetic groups. CONCLUSION Results revealed that DNA methylation plays a causal role in the effectiveness of the isolated OF. Furthermore, the possible regenerative potential of oligosaccharide in diabetic rats may have contributed to the modulation of DNA methylation.
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Affiliation(s)
- Gholamreza Bahrami
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
- School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Soraya Sajadimajd
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Bahareh Mohammadi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Razieh Hatami
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Shahram Miraghaee
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Samira Keshavarzi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mozafar Khazaei
- Fertility and Infertility Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Seyed Hamid Madani
- Molecular Pathology Research Center, Clinical Research Development Center, Imam Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah, Iran
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99972
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Xie W, Sowemimo I, Hayashi R, Wang J, Burkard TR, Brennecke J, Ameres SL, Patel DJ. Structure-function analysis of microRNA 3'-end trimming by Nibbler. Proc Natl Acad Sci U S A 2020; 117:30370-30379. [PMID: 33199607 PMCID: PMC7720153 DOI: 10.1073/pnas.2018156117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Nibbler (Nbr) is a 3'-to-5' exoribonuclease whose catalytic 3'-end trimming activity impacts microRNA (miRNA) and PIWI-interacting RNA (piRNA) biogenesis. Here, we report on structural and functional studies to decipher the contributions of Nbr's N-terminal domain (NTD) and exonucleolytic domain (EXO) in miRNA 3'-end trimming. We have solved the crystal structures of the NTD core and EXO domains of Nbr, both in the apo-state. The NTD-core domain of Aedes aegypti Nbr adopts a HEAT-like repeat scaffold with basic patches constituting an RNA-binding surface exhibiting a preference for binding double-strand RNA (dsRNA) over single-strand RNA (ssRNA). Structure-guided functional assays in Drosophila S2 cells confirmed a principal role of the NTD in exonucleolytic miRNA trimming, which depends on basic surface patches. Gain-of-function experiments revealed a potential role of the NTD in recruiting Nbr to Argonaute-bound small RNA substrates. The EXO domain of A. aegypti and Drosophila melanogaster Nbr adopt a mixed α/β-scaffold with a deep pocket lined by a DEDDy catalytic cleavage motif. We demonstrate that Nbr's EXO domain exhibits Mn2+-dependent ssRNA-specific 3'-to-5' exoribonuclease activity. Modeling of a 3' terminal Uridine into the catalytic pocket of Nbr EXO indicates that 2'-O-methylation of the 3'-U would result in a steric clash with a tryptophan side chain, suggesting that 2'-O-methylation protects small RNAs from Nbr-mediated trimming. Overall, our data establish that Nbr requires its NTD as a substrate recruitment platform to execute exonucleolytic miRNA maturation, catalyzed by the ribonuclease EXO domain.
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Affiliation(s)
- Wei Xie
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Ivica Sowemimo
- Institute of Molecular Biotechnology, Vienna BioCenter, 1030 Vienna, Austria
| | - Rippei Hayashi
- Department of Genome Sciences, The John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia
| | - Juncheng Wang
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Thomas R Burkard
- Institute of Molecular Biotechnology, Vienna BioCenter, 1030 Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology, Vienna BioCenter, 1030 Vienna, Austria;
| | - Stefan L Ameres
- Institute of Molecular Biotechnology, Vienna BioCenter, 1030 Vienna, Austria;
- Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065;
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99973
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Kapli P, Telford MJ. Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha. Sci Adv 2020; 6:eabc5162. [PMID: 33310849 PMCID: PMC7732190 DOI: 10.1126/sciadv.abc5162] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/27/2020] [Indexed: 05/21/2023]
Abstract
The evolutionary relationships of two animal phyla, Ctenophora and Xenacoelomorpha, have proved highly contentious. Ctenophora have been proposed as the most distant relatives of all other animals (Ctenophora-first rather than the traditional Porifera-first). Xenacoelomorpha may be primitively simple relatives of all other bilaterally symmetrical animals (Nephrozoa) or simplified relatives of echinoderms and hemichordates (Xenambulacraria). In both cases, one of the alternative topologies must be a result of errors in tree reconstruction. Here, using empirical data and simulations, we show that the Ctenophora-first and Nephrozoa topologies (but not Porifera-first and Ambulacraria topologies) are strongly supported by analyses affected by systematic errors. Accommodating this finding suggests that empirical studies supporting Ctenophora-first and Nephrozoa trees are likely to be explained by systematic error. This would imply that the alternative Porifera-first and Xenambulacraria topologies, which are supported by analyses designed to minimize systematic error, are the most credible current alternatives.
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Affiliation(s)
- Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
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99974
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Park JS, Jin DP, Choi BH. Insights into genomic structure and evolutionary processes of coastal Suaeda species in East Asia using cpDNA, nDNA, and genome-wide SNPs. Sci Rep 2020; 10:20950. [PMID: 33262390 PMCID: PMC7708624 DOI: 10.1038/s41598-020-78041-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/27/2020] [Indexed: 11/30/2022] Open
Abstract
Species in the genus Suaeda have few diagnostic characters and substantial morphological plasticity. Hence, regional floras do not provide clear taxonomic information for Suaeda spp. in East Asia. In order to assess the taxonomy of four species in the genus Suaeda (S. australis, S. maritima, S. japonica, and S. heteroptera), cpDNA (rpl32-trnL and trnH-psbA), nDNA (ITS), and MIG-seq analyses were carried out. Genome-wide SNP results indicated three lineages: (1) S. australis in Korea and S. maritima in Japan, (2) S. maritima in Korea and S. heteroptera in China, and (3) S. japionica. In phylogenetic trees and genotype analyses, cpDNA and nDNA results showed discrepancies, while S. japonica and S. maritima in Korea, and S. heteroptera in China shared the same haplotype and ribotype. We suggest that the shared haplotype may be due to chloroplast capture. Based on our results, we assume that S. japonica was formed by homoploid hybrid speciation between the two lineages.
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Affiliation(s)
- Jong-Soo Park
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Dong-Pil Jin
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Byoung-Hee Choi
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea.
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99975
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Zhang D, Liu C, Li H, Jiao J. Deficiency of STING Signaling in Embryonic Cerebral Cortex Leads to Neurogenic Abnormalities and Autistic-Like Behaviors. Adv Sci (Weinh) 2020; 7:2002117. [PMID: 33304758 PMCID: PMC7710002 DOI: 10.1002/advs.202002117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/14/2020] [Indexed: 05/27/2023]
Abstract
STING is known as a central adaptor for sensing cytosolic DNA sensing. Recent studies have provided evidence that STING response is divergent among different cell types. Here, this work demonstrates that STING controls neural progenitor cells (NPCs) by sensing DNA damage in NPCs. The deletion of STING reduces neuronal differentiation and increases proliferation of mouse and human NPCs. Furthermore, STINGcKO mice display autistic-like behaviors. In NPCs, STING specifically recruits IKKβ and activates nuclear factor κB (NF-κB) through phosphorylation. NF-κB binds to ALX4 promoter and triggers ALX4 transcription. In addition, tumor necrosis factor α, an activator of NF-κB, can rescue some phenotypes caused by STING deletion in mice. Together, the findings show that STING signaling is essential for neuronal gene expression program and has profound consequences on brain function.
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Affiliation(s)
- Dongming Zhang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- Medical SchoolUniversity of Chinese Academy of SciencesBeijing100049China
| | - Chang Liu
- Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
| | - Hong Li
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- Medical SchoolUniversity of Chinese Academy of SciencesBeijing100049China
- Innovation Academy for Stem Cell and RegenerationBeijing100101China
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99976
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Browning AP, Warne DJ, Burrage K, Baker RE, Simpson MJ. Identifiability analysis for stochastic differential equation models in systems biology. J R Soc Interface 2020; 17:20200652. [PMID: 33323054 PMCID: PMC7811582 DOI: 10.1098/rsif.2020.0652] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/24/2020] [Indexed: 12/26/2022] Open
Abstract
Mathematical models are routinely calibrated to experimental data, with goals ranging from building predictive models to quantifying parameters that cannot be measured. Whether or not reliable parameter estimates are obtainable from the available data can easily be overlooked. Such issues of parameter identifiability have important ramifications for both the predictive power of a model, and the mechanistic insight that can be obtained. Identifiability analysis is well-established for deterministic, ordinary differential equation (ODE) models, but there are no commonly adopted methods for analysing identifiability in stochastic models. We provide an accessible introduction to identifiability analysis and demonstrate how existing ideas for analysis of ODE models can be applied to stochastic differential equation (SDE) models through four practical case studies. To assess structural identifiability, we study ODEs that describe the statistical moments of the stochastic process using open-source software tools. Using practically motivated synthetic data and Markov chain Monte Carlo methods, we assess parameter identifiability in the context of available data. Our analysis shows that SDE models can often extract more information about parameters than deterministic descriptions. All code used to perform the analysis is available on Github.
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Affiliation(s)
- Alexander P. Browning
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane, Australia
| | - David J. Warne
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane, Australia
| | - Kevin Burrage
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Queensland University of Technology, Brisbane, Australia
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Ruth E. Baker
- Mathematical Institute, University of Oxford, Oxford, UK
| | - Matthew J. Simpson
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane, Australia
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99977
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Luna PN, Mansbach JM, Shaw CA. A joint modeling approach for longitudinal microbiome data improves ability to detect microbiome associations with disease. PLoS Comput Biol 2020; 16:e1008473. [PMID: 33315858 PMCID: PMC7769610 DOI: 10.1371/journal.pcbi.1008473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 12/28/2020] [Accepted: 10/27/2020] [Indexed: 02/02/2023] Open
Abstract
Changes in the composition of the microbiome over time are associated with myriad human illnesses. Unfortunately, the lack of analytic techniques has hindered researchers' ability to quantify the association between longitudinal microbial composition and time-to-event outcomes. Prior methodological work developed the joint model for longitudinal and time-to-event data to incorporate time-dependent biomarker covariates into the hazard regression approach to disease outcomes. The original implementation of this joint modeling approach employed a linear mixed effects model to represent the time-dependent covariates. However, when the distribution of the time-dependent covariate is non-Gaussian, as is the case with microbial abundances, researchers require different statistical methodology. We present a joint modeling framework that uses a negative binomial mixed effects model to determine longitudinal taxon abundances. We incorporate these modeled microbial abundances into a hazard function with a parameterization that not only accounts for the proportional nature of microbiome data, but also generates biologically interpretable results. Herein we demonstrate the performance improvements of our approach over existing alternatives via simulation as well as a previously published longitudinal dataset studying the microbiome during pregnancy. The results demonstrate that our joint modeling framework for longitudinal microbiome count data provides a powerful methodology to uncover associations between changes in microbial abundances over time and the onset of disease. This method offers the potential to equip researchers with a deeper understanding of the associations between longitudinal microbial composition changes and disease outcomes. This new approach could potentially lead to new diagnostic biomarkers or inform clinical interventions to help prevent or treat disease.
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Affiliation(s)
- Pamela N. Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Statistics, Rice University, Houston, Texas, United States of America
| | - Jonathan M. Mansbach
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Statistics, Rice University, Houston, Texas, United States of America
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99978
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Zrimec J, Börlin CS, Buric F, Muhammad AS, Chen R, Siewers V, Verendel V, Nielsen J, Töpel M, Zelezniak A. Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. Nat Commun 2020; 11:6141. [PMID: 33262328 PMCID: PMC7708451 DOI: 10.1038/s41467-020-19921-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 11/02/2020] [Indexed: 12/31/2022] Open
Abstract
Understanding the genetic regulatory code governing gene expression is an important challenge in molecular biology. However, how individual coding and non-coding regions of the gene regulatory structure interact and contribute to mRNA expression levels remains unclear. Here we apply deep learning on over 20,000 mRNA datasets to examine the genetic regulatory code controlling mRNA abundance in 7 model organisms ranging from bacteria to Human. In all organisms, we can predict mRNA abundance directly from DNA sequence, with up to 82% of the variation of transcript levels encoded in the gene regulatory structure. By searching for DNA regulatory motifs across the gene regulatory structure, we discover that motif interactions could explain the whole dynamic range of mRNA levels. Co-evolution across coding and non-coding regions suggests that it is not single motifs or regions, but the entire gene regulatory structure and specific combination of regulatory elements that define gene expression levels.
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Affiliation(s)
- Jan Zrimec
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Christoph S Börlin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Filip Buric
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Azam Sheikh Muhammad
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Rhongzen Chen
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Vilhelm Verendel
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Mats Töpel
- Department of Marine Sciences, University of Gothenburg, Box 461, SE-405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center (GGBC), Box 461, 40530, Gothenburg, Sweden
| | - Aleksej Zelezniak
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23a, SE-171 65, Stockholm, Sweden.
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99979
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Harrington NE, Sweeney E, Harrison F. Building a better biofilm - Formation of in vivo-like biofilm structures by Pseudomonas aeruginosa in a porcine model of cystic fibrosis lung infection. Biofilm 2020; 2:100024. [PMID: 33381751 PMCID: PMC7762787 DOI: 10.1016/j.bioflm.2020.100024] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/24/2020] [Accepted: 04/24/2020] [Indexed: 12/20/2022] Open
Abstract
Pseudomonas aeruginosa biofilm infections in the cystic fibrosis (CF) lung are highly resistant to current antimicrobial treatments and are associated with increased mortality rates. The existing models for such infections are not able to reliably mimic the clinical biofilms observed. We aimed to further optimise an ex vivo pig lung (EVPL) model for P. aeruginosa CF lung infection that can be used to increase understanding of chronic CF biofilm infection. The EVPL model will facilitate discovery of novel infection prevention methods and treatments, and enhanced exploration of biofilm architecture. We investigated purine metabolism and biofilm formation in the model using transposon insertion mutants in P. aeruginosa PA14 for key genes: purD, gacA and pelA. Our results demonstrate that EVPL recapitulates a key aspect of in vivo P. aeruginosa infection metabolism, and that the pathogen forms a biofilm with a clinically realistic structure not seen in other in vitro studies. Two pathways known to be required for in vivo biofilm infection - the Gac regulatory pathway and production of the Pel exopolysaccharide - are essential to the formation of this mature, structured biofilm on EVPL tissue. We propose the high-throughput EVPL model as a validated biofilm platform to bridge the gap between in vitro work and CF lung infection.
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Affiliation(s)
- Niamh E. Harrington
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Esther Sweeney
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Freya Harrison
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, United Kingdom
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99980
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Pearman WS, Wells SJ, Silander OK, Freed NE, Dale J. Concordant geographic and genetic structure revealed by genotyping-by-sequencing in a New Zealand marine isopod. Ecol Evol 2020; 10:13624-13639. [PMID: 33391668 PMCID: PMC7771188 DOI: 10.1002/ece3.6802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/19/2022] Open
Abstract
Population genetic structure in the marine environment can be influenced by life-history traits such as developmental mode (biphasic, with distinct adult and larval morphology, and direct development, in which larvae resemble adults) or habitat specificity, as well as geography and selection. Developmental mode is thought to significantly influence dispersal, with direct developers expected to have much lower dispersal potential. However, this prediction can be complicated by the presence of geophysical barriers to dispersal. In this study, we use a panel of 8,020 SNPs to investigate population structure and biogeography over multiple spatial scales for a direct-developing species, the New Zealand endemic marine isopod Isocladus armatus. Because our sampling range is intersected by two well-known biogeographic barriers (the East Cape and the Cook Strait), our study provides an opportunity to understand how such barriers influence dispersal in direct developers. On a small spatial scale (20 km), gene flow between locations is extremely high, suggestive of an island model of migration. However, over larger spatial scales (600 km), populations exhibit a clear pattern of isolation-by-distance. Our results indicate that I. armatus exhibits significant migration across the hypothesized barriers and suggest that large-scale ocean currents associated with these locations do not present a barrier to dispersal. Interestingly, we find evidence of a north-south population genetic break occurring between Māhia and Wellington. While no known geophysical barrier is apparent in this area, it coincides with the location of a proposed border between bioregions. Analysis of loci under selection revealed that both isolation-by-distance and adaption may be contributing to the degree of population structure we have observed here. We conclude that developmental life history largely predicts dispersal in the intertidal isopod I. armatus. However, localized biogeographic processes can disrupt this expectation, and this may explain the potential meta-population detected in the Auckland region.
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Affiliation(s)
- William S. Pearman
- School of Natural and Computational SciencesMassey UniversityAucklandNew Zealand
| | - Sarah J. Wells
- School of Environmental and Animal SciencesUnitec Institute of TechnologyAucklandNew Zealand
| | - Olin K. Silander
- School of Natural and Computational SciencesMassey UniversityAucklandNew Zealand
| | - Nikki E. Freed
- School of Natural and Computational SciencesMassey UniversityAucklandNew Zealand
| | - James Dale
- School of Natural and Computational SciencesMassey UniversityAucklandNew Zealand
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99981
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Tian B, Xie J, Fu Y, Cheng J, Li B, Chen T, Zhao Y, Gao Z, Yang P, Barbetti MJ, Tyler BM, Jiang D. A cosmopolitan fungal pathogen of dicots adopts an endophytic lifestyle on cereal crops and protects them from major fungal diseases. ISME J 2020; 14:3120-3135. [PMID: 32814863 PMCID: PMC7784893 DOI: 10.1038/s41396-020-00744-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/30/2020] [Accepted: 08/07/2020] [Indexed: 11/09/2022]
Abstract
Fungal pathogens are seriously threatening food security and natural ecosystems; efficient and environmentally friendly control methods are essential to help safeguard such resources for increasing human populations on a global scale. Here, we find that Sclerotinia sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, rice, barley, maize, and oat, providing protection against Fusarium head blight, stripe rust, and rice blast. Protection is also provided by disabled S. sclerotiorum strains harboring a hypovirulence virus. The disabled strain DT-8 promoted wheat yields by 4-18% in the field and consistently reduced Fusarium disease by 40-60% across multiple field trials. We term the host-dependent trophism of S. sclerotiorum, destructively pathogenic or mutualistically endophytic, as schizotrophism. As a biotroph, S. sclerotiorum modified the expression of wheat genes involved in disease resistance and photosynthesis and increased the level of IAA. Our study shows that a broad-spectrum pathogen of one group of plants may be employed as a biocontrol agent in a different group of plants where they can be utilized as beneficial microorganisms while avoiding the risk of in-field release of pathogens. Our study also raises provocative questions about the potential role of schizotrophic endophytes in natural ecosystems.
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Affiliation(s)
- Binnian Tian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Tao Chen
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Ying Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Zhixiao Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Puyun Yang
- National Agro-Technical Extension and Service Center, Ministry of Agriculture and Rural Affairs, Beijing, China
- Research and Extension Unit, Agriculture and Consumer Protection Department, Food and Agriculture Organisation of the United Nations, Rome, Italy
| | - Martin J Barbetti
- The UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Brett M Tyler
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China.
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99982
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Francis M, Gopinathan G, Salapatas A, Nares S, Gonzalez M, Diekwisch T, Luan X. SETD1 and NF-κB Regulate Periodontal Inflammation through H3K4 Trimethylation. J Dent Res 2020; 99:1486-1493. [PMID: 32762504 PMCID: PMC7684838 DOI: 10.1177/0022034520939029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The inflammatory response to periodontal pathogens is dynamically controlled by the chromatin state on inflammatory gene promoters. In the present study, we have focused on the effect of the methyltransferase SETD1B on histone H3 lysine K4 (H3K4) histone trimethylation on inflammatory gene promoters. Experiments were based on 3 model systems: 1) an in vitro periodontal ligament (PDL) cell culture model for the study of SETD1 function as it relates to histone methylation and inflammatory gene expression using Porphyromonas gingivalis lipopolysaccharide (LPS) as a pathogen, 2) a subcutaneous implantation model to determine the relationship between SETD1 and nuclear factor κB (NF-κB) through its activation inhibitor BOT-64, and 3) a mouse periodontitis model to test whether the NF-κB activation inhibitor BOT-64 reverses the inflammatory tissue destruction associated with periodontal disease. In our PDL progenitor cell culture model, P. gingivalis LPS increased H3K4me3 histone methylation on IL-1β, IL-6, and MMP2 gene promoters, while SETD1B inhibition decreased H3K4me3 enrichment and inflammatory gene expression in LPS-treated PDL cells. LPS also increased SETD1 nuclear localization in a p65-dependent fashion and the nuclear translocation of p65 as mediated through SETD1, suggestive of a synergistic effect between SETD1 and p65 in the modulation of inflammation. Confirming the role of SETD1 in p65-mediated periodontal inflammation, BOT-64 reduced the number of SETD1-positive cells in inflamed periodontal tissues, restored periodontal tissue integrity, and enhanced osteogenesis in a periodontal inflammation model in vivo. Together, these results have established the histone lysine methyltransferase SETD1 as a key factor in the opening of the chromatin on inflammatory gene promoters through histone H3K4 trimethylation. Our studies also confirmed the role of BOT-64 as a potent molecular therapeutic for the restoration of periodontal health through the inhibition of NF-κB activity and the amelioration of SETD1-induced chromatin relaxation.
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Affiliation(s)
- M. Francis
- Department of Oral Biology, UIC College of Dentistry, Chicago, IL, USA
| | - G. Gopinathan
- Department of Periodontics and Center for Craniofacial Research and Diagnosis, Texas A&M University College of Dentistry, Dallas, TX, USA
| | - A. Salapatas
- Department of Oral Biology, UIC College of Dentistry, Chicago, IL, USA
| | - S. Nares
- Department of Periodontics, UIC College of Dentistry, Chicago, IL, USA
| | - M. Gonzalez
- Department of Periodontics and Center for Craniofacial Research and Diagnosis, Texas A&M University College of Dentistry, Dallas, TX, USA
| | - T.G.H. Diekwisch
- Department of Oral Biology, UIC College of Dentistry, Chicago, IL, USA
- Department of Periodontics and Center for Craniofacial Research and Diagnosis, Texas A&M University College of Dentistry, Dallas, TX, USA
| | - X. Luan
- Department of Oral Biology, UIC College of Dentistry, Chicago, IL, USA
- Department of Periodontics and Center for Craniofacial Research and Diagnosis, Texas A&M University College of Dentistry, Dallas, TX, USA
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99983
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de Gannes M, Ko CI, Zhang X, Biesiada J, Niu L, Koch SE, Medvedovic M, Rubinstein J, Puga A. Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes That Govern Cardiomyocyte Maturation. Toxicol Sci 2020; 178:325-337. [PMID: 33017471 DOI: 10.1093/toxsci/kfaa153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Congenital heart disease (CHD), the leading birth defect worldwide, has a largely unknown etiology, likely to result from complex interactions between genetic and environmental factors during heart development, at a time when the heart adapts to diverse physiological and pathophysiological conditions. Crucial among these is the regulation of cardiomyocyte development and postnatal maturation, governed by dynamic changes in DNA methylation. Previous work from our laboratory has shown that exposure to the environmental toxicant tetrachlorodibenzo-p-dioxin (TCDD) disrupts several molecular networks responsible for heart development and function. To test the hypothesis that the disruption caused by TCDD in the heart results from changes in DNA methylation and gene expression patterns of cardiomyocytes, we established a stable mouse embryonic stem cell line expressing a puromycin resistance selectable marker under control of the cardiomyocyte-specific Nkx2-5 promoter. Differentiation of these cells in the presence of puromycin induces the expression of a large suite of cardiomyocyte-specific markers. To assess the consequences of TCDD treatment on gene expression and DNA methylation in these cardiomyocytes, we subjected them to transcriptome and methylome analyses in the presence of TCDD. Unlike control cardiomyocytes maintained in vehicle, the TCDD-treated cardiomyocytes showed extensive gene expression changes, with a significant correlation between differential RNA expression and DNA methylation in 111 genes, many of which are key elements of pathways that regulate cardiovascular development and function. Our findings provide an important clue toward the elucidation of the complex interactions between genetic and epigenetic mechanisms after developmental TCDD exposure that may contribute to CHD.
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Affiliation(s)
- Matthew de Gannes
- Department of Environmental Health and Center for Environmental Genetics
| | - Chia-I Ko
- Department of Environmental Health and Center for Environmental Genetics
| | - Xiang Zhang
- Department of Environmental Health and Center for Environmental Genetics
| | - Jacek Biesiada
- Department of Environmental Health and Center for Environmental Genetics
| | - Liang Niu
- Department of Environmental Health and Center for Environmental Genetics
| | - Sheryl E Koch
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267
| | - Mario Medvedovic
- Department of Environmental Health and Center for Environmental Genetics
| | - Jack Rubinstein
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267
| | - Alvaro Puga
- Department of Environmental Health and Center for Environmental Genetics
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99984
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Dermauw W, Van Leeuwen T, Feyereisen R. Diversity and evolution of the P450 family in arthropods. Insect Biochem Mol Biol 2020; 127:103490. [PMID: 33169702 DOI: 10.1016/j.ibmb.2020.103490] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 05/13/2023]
Abstract
The P450 family (CYP genes) of arthropods encodes diverse enzymes involved in the metabolism of foreign compounds and in essential endocrine or ecophysiological functions. The P450 sequences (CYPome) from 40 arthropod species were manually curated, including 31 complete CYPomes, and a maximum likelihood phylogeny of nearly 3000 sequences is presented. Arthropod CYPomes are assembled from members of six CYP clans of variable size, the CYP2, CYP3, CYP4 and mitochondrial clans, as well as the CYP20 and CYP16 clans that are not found in Neoptera. CYPome sizes vary from two dozen genes in some parasitic species to over 200 in species as diverse as collembolans or ticks. CYPomes are comprised of few CYP families with many genes and many CYP families with few genes, and this distribution is the result of dynamic birth and death processes. Lineage-specific expansions or blooms are found throughout the phylogeny and often result in genomic clusters that appear to form a reservoir of catalytic diversity maintained as heritable units. Among the many P450s with physiological functions, six CYP families are involved in ecdysteroid metabolism. However, five so-called Halloween genes are not universally represented and do not constitute the unique pathway of ecdysteroid biosynthesis. The diversity of arthropod CYPomes has only partially been uncovered to date and many P450s with physiological functions regulating the synthesis and degradation of endogenous signal molecules (including ecdysteroids) and semiochemicals (including pheromones and defense chemicals) remain to be discovered. Sequence diversity of arthropod P450s is extreme, and P450 sequences lacking the universally conserved Cys ligand to the heme have evolved several times. A better understanding of P450 evolution is needed to discern the relative contributions of stochastic processes and adaptive processes in shaping the size and diversity of CYPomes.
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Affiliation(s)
- Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - René Feyereisen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium; Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871, Frederiksberg C, Copenhagen, Denmark.
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99985
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Abstract
Base editing - the introduction of single-nucleotide variants (SNVs) into DNA or RNA in living cells - is one of the most recent advances in the field of genome editing. As around half of known pathogenic genetic variants are due to SNVs, base editing holds great potential for the treatment of numerous genetic diseases, through either temporary RNA or permanent DNA base alterations. Recent advances in the specificity, efficiency, precision and delivery of DNA and RNA base editors are revealing exciting therapeutic opportunities for these technologies. We expect the correction of single point mutations will be a major focus of future precision medicine.
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Affiliation(s)
- Elizabeth M Porto
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
| | - Ian M Slaymaker
- Synthetic Biology Department, Beam Therapeutics, Cambridge, MA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Biomedical Sciences and Bioinformatics and Systems Biology Graduate Programs, University of California, San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
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99986
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Lammers NC, Kim YJ, Zhao J, Garcia HG. A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting. Curr Opin Cell Biol 2020; 67:147-157. [PMID: 33242838 PMCID: PMC8498946 DOI: 10.1016/j.ceb.2020.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/03/2020] [Indexed: 12/18/2022]
Abstract
Eukaryotic transcription generally occurs in bursts of activity lasting minutes to hours; however, state-of-the-art measurements have revealed that many of the molecular processes that underlie bursting, such as transcription factor binding to DNA, unfold on timescales of seconds. This temporal disconnect lies at the heart of a broader challenge in physical biology of predicting transcriptional outcomes and cellular decision-making from the dynamics of underlying molecular processes. Here, we review how new dynamical information about the processes underlying transcriptional control can be combined with theoretical models that predict not only averaged transcriptional dynamics, but also their variability, to formulate testable hypotheses about the molecular mechanisms underlying transcriptional bursting and control.
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Affiliation(s)
- Nicholas C Lammers
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA
| | - Yang Joon Kim
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA
| | - Jiaxi Zhao
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA; Department of Physics, University of California at Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, USA.
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99987
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To TK, Nishizawa Y, Inagaki S, Tarutani Y, Tominaga S, Toyoda A, Fujiyama A, Berger F, Kakutani T. RNA interference-independent reprogramming of DNA methylation in Arabidopsis. Nat Plants 2020; 6:1455-1467. [PMID: 33257860 DOI: 10.1038/s41477-020-00810-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/16/2020] [Indexed: 06/12/2023]
Abstract
DNA methylation is important for silencing transposable elements (TEs) in diverse eukaryotes, including plants. In plant genomes, TEs are silenced by methylation of histone H3 lysine 9 (H3K9) and cytosines in both CG and non-CG contexts. The role of RNA interference (RNAi) in establishing TE-specific silent marks has been extensively studied, but the importance of RNAi-independent pathways remains largely unexplored. Here, we directly investigated transgenerational de novo DNA methylation of TEs after the loss of silent marks. Our analyses uncovered potent and precise RNAi-independent pathways for recovering non-CG methylation and H3K9 methylation in most TE genes (that is, coding regions within TEs). Characterization of a subset of TE genes without the recovery revealed the effects of H3K9 demethylation, replacement of histone H2A variants and their interaction with CG methylation, together with feedback from transcription. These chromatin components are conserved among eukaryotes and may contribute to chromatin reprogramming in a conserved manner.
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Affiliation(s)
- Taiko Kim To
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan.
| | - Yuichiro Nishizawa
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Soichi Inagaki
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
- Department of Integrated Genetics, National Institute of Genetics (NIG), Mishima, Shizuoka, Japan
- PREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Yoshiaki Tarutani
- Department of Integrated Genetics, National Institute of Genetics (NIG), Mishima, Shizuoka, Japan
| | - Sayaka Tominaga
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Atsushi Toyoda
- Center for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Center for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Tetsuji Kakutani
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan.
- Department of Integrated Genetics, National Institute of Genetics (NIG), Mishima, Shizuoka, Japan.
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99988
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Hannaford NE, Heaps SE, Nye TMW, Williams TA, Embley TM. Incorporating compositional heterogeneity into Lie Markov models for phylogenetic inference. Ann Appl Stat 2020. [DOI: 10.1214/20-aoas1369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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99989
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99990
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Wium-Andersen MK, Dalgaard Villumsen M, Wium-Andersen IK, Jørgensen MB, Hjelmborg JB, Christensen K, Osler M. Familial risk and heritability of depression by age at first diagnosis in Danish twins. Acta Psychiatr Scand 2020; 142:446-455. [PMID: 33010028 DOI: 10.1111/acps.13238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Familial and genetic factors seem to contribute to the development of depression but whether this varies with age at diagnosis remains unclear. We examined the influence of familial factors on the risk of depression by age at first diagnosis. METHODS We included 23 498 monozygotic and 39 540 same-sex dizygotic twins from the population-based Danish Twin Registry, followed from 1977 through 2011 in nationwide registers. We used time-to-event analyses accounting for censoring and competing risk of death to estimate cumulative incidence, casewise concordance, relative recurrence risk, and heritability of first depression by age using monozygotic and same-sex dizygotic twin pairs. RESULTS During follow-up, a total of 1545 twins were diagnosed with depression. For twins at age 35 or younger at first depression, heritability was estimated to be 24.8% (95% confidence interval [CI], 4.6-43.1%), whereas at age 90 it was 14.7% (95% CI, 3.1-26.3%). The relative recurrence risk was higher at younger ages: At age 35, the risk was 27.7-fold (95% CI, 20.0-35.5) and 6.9-fold (95% CI, 3.9-9.8) higher than the population risk for monozygotic and same-sex dizygotic twins, respectively, while the corresponding numbers were 3.0 (95% CI, 2.3-3.6) and 1.8 (95% CI, 1.3-2.2) at age 90. Heritability seemed similar for male and female twins. CONCLUSION Familial risk of depression, caused either by genes or shared environment, seemed to slightly decrease with age at diagnosis and an elevated concordance risk for monozygotic over same-sex dizygotic pairs suggested a genetic contribution to the development of depression.
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Affiliation(s)
- M K Wium-Andersen
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, Denmark
| | - M Dalgaard Villumsen
- Department of Epidemiology, Biostatistics, and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark.,The Danish Twin Registry, University of Southern Denmark, Odense, Denmark
| | | | - M B Jørgensen
- Psychiatric Center Copenhagen, Rigshospital, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Kobenhavns, Denmark
| | - J B Hjelmborg
- Department of Epidemiology, Biostatistics, and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark.,The Danish Twin Registry, University of Southern Denmark, Odense, Denmark
| | - K Christensen
- Department of Epidemiology, Biostatistics, and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark.,The Danish Twin Registry, University of Southern Denmark, Odense, Denmark
| | - M Osler
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, Denmark.,Department of Public Health, Section of Epidemiology, University of Copenhagen, Kobenhavns, Denmark
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99991
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Hosoya A, Shalehin N, Takebe H, Fujii S, Seki Y, Mizoguchi T, Shimo T, Iijima M, Irie K. Stem cell properties of Gli1-positive cells in the periodontal ligament. J Oral Biosci 2020; 62:299-305. [DOI: 10.1016/j.job.2020.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/14/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022]
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99992
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Monaco A, Pantaleo E, Amoroso N, Bellantuono L, Lombardi A, Tateo A, Tangaro S, Bellotti R. Identifying potential gene biomarkers for Parkinson's disease through an information entropy based approach. Phys Biol 2020; 18:016003. [PMID: 33049726 DOI: 10.1088/1478-3975/abc09a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Parkinson's disease (PD) is a chronic, progressive neurodegenerative disease and represents the most common disease of this type, after Alzheimer's dementia. It is characterized by motor and nonmotor features and by a long prodromal stage that lasts many years. Genetic research has shown that PD is a complex and multisystem disorder. To capture the molecular complexity of this disease we used a complex network approach. We maximized the information entropy of the gene co-expression matrix betweenness to obtain a gene adjacency matrix; then we used a fast greedy algorithm to detect communities. Finally we applied principal component analysis on the detected gene communities, with the ultimate purpose of discriminating between PD patients and healthy controls by means of a random forests classifier. We used a publicly available substantia nigra microarray dataset, GSE20163, from NCBI GEO database, containing gene expression profiles for 10 PD patients and 18 normal controls. With this methodology we identified two gene communities that discriminated between the two groups with mean accuracy of 0.88 ± 0.03 and 0.84 ± 0.03, respectively, and validated our results on an independent microarray experiment. The two gene communities presented a considerable reduction in size, over 100 times, compared to the initial network and were stable within a range of tested parameters. Further research focusing on the restricted number of genes belonging to the selected communities may reveal essential mechanisms responsible for PD at a network level and could contribute to the discovery of new biomarkers for PD.
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Affiliation(s)
- A Monaco
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, Italy
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99993
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Chong X, Guan Y, Jiang J, Zhang F, Wang H, Song A, Chen S, Ding L, Chen F. Heterologous expression of chrysanthemum TOPLESS corepressor CmTPL1-1 alters meristem maintenance and organ development in Arabidopsis thaliana. Plant Physiol Biochem 2020; 157:256-263. [PMID: 33152644 DOI: 10.1016/j.plaphy.2020.10.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
TOPLESS (TPL)/TOPLESS-related (TPR) corepressors are important regulators of plant growth and development, but their functions in chrysanthemum (Chrysanthemum morifolium) are currently unclear. In this study, a chrysanthemum TPL/TPR family gene, designated CmTPL1-1, was characterized. This gene encodes an 1135-amino-acid polypeptide harboring a conserved N-terminal domain and two C-terminal WD40 domains. CmTPL1-1 showed no transcriptional activity in yeast, and a localization experiment indicated that it localized to the nuclei in onion epidermal cells. Transcript profiling established that the gene was most highly expressed in the stem apex. The heterologous expression of CmTPL1-1 in Arabidopsis thaliana produced a pleiotropic phenotype, including smaller leaves, shorter siliques, increased meristem number, asymmetrical petal distribution and reduced stamen number. In transgenic plants, four AtARFs were downregulated, while six AtIAAs and two AtGH3s were upregulated at the transcript level; moreover, the expression of three key class I KNOTTED-like homeobox (KNOX) genes was upregulated. In addition, by yeast two-hybrid screening of a chrysanthemum cDNA library, we found that CmTPL1-1 could interact with CmWOX4, CmLBD38 and CmLBD36, and these interactions were confirmed by bimolecular fluorescence complementation (BiFC) assays. Overall, we speculated that heterologous expression of CmTPL1-1 regulates plant growth and development by interacting with auxin signaling in Arabidopsis.
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Affiliation(s)
- Xinran Chong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yunxiao Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Fei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Haibin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Lian Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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99994
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Sikora E, Czarnecka-herok J, Bojko A, Sunderland P. Therapy-induced polyploidization and senescence: Coincidence or interconnection? Semin Cancer Biol 2020. [DOI: 10.1016/j.semcancer.2020.11.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023]
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99995
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El-Said YAM, Sallam NAA, Ain-Shoka AAM, Abdel-Latif HAT. Geraniol ameliorates diabetic nephropathy via interference with miRNA-21/PTEN/Akt/mTORC1 pathway in rats. Naunyn Schmiedebergs Arch Pharmacol 2020; 393:2325-2337. [PMID: 32666288 DOI: 10.1007/s00210-020-01944-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022]
Abstract
Deregulated activity of protein kinase B/mammalian target of rapamycin complex-1 (Akt/mTORC1) incites crucial pathological characteristics of diabetic nephropathy. The acyclic monoterpene geraniol has been recently reported to possess antidiabetic effects; however, its potential renoprotective effect in diabetes has not yet been elucidated. This study aimed to assess the possible modulatory effect of geraniol on the Akt/mTORC1 pathway in diabetes-induced nephropathy in rats compared to the standard antidiabetic drug gliclazide. Geraniol and gliclazide was administered daily to diabetic rats for 6 weeks starting on the 3rd-day post diabetes induction by streptozotocin (STZ). Geraniol amended the deteriorated renal function (serum creatinine; blood urea nitrogen). It exerted a remarkable antihyperglycemic effect that is comparable to that of gliclazide and suppressed the fibrotic marker, transforming growth factor-β. Geraniol restored redox balance and inhibited lipid peroxidation by reducing nicotine amide adenine dinucleotide phosphate oxidase and enhancing the antioxidant enzyme, superoxide dismutase. These beneficial effects were associated with a robust downregulation of miRNA-21 and consequently, reversion of tumor suppressor protein phosphatase and tension homolog (PTEN)/Akt/mTORC1 cue and its downstream proteins required for mesangial cell proliferation and matrix protein synthesis. The current study indicates that geraniol interfered with miRNA-21/ PTEN/AKT/mTORC1 pathway signaling that contributes largely to the progression of mesangial expansion and extracellular matrix deposition in diabetic nephropathy.
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99996
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Alkotob SS, Cannedy C, Harter K, Movassagh H, Paudel B, Prunicki M, Sampath V, Schikowski T, Smith E, Zhao Q, Traidl‐Hoffmann C, Nadeau KC. Advances and novel developments in environmental influences on the development of atopic diseases. Allergy 2020; 75:3077-3086. [PMID: 33037680 DOI: 10.1111/all.14624] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022]
Abstract
Although genetic factors play a role in the etiology of atopic disease, the rapid increases in the prevalence of these diseases over the last few decades suggest that environmental, rather than genetic factors are the driving force behind the increasing prevalence. In modern societies, there is increased time spent indoors, use of antibiotics, and consumption of processed foods and decreased contact with farm animals and pets, which limit exposure to environmental allergens, infectious parasitic worms, and microbes. The lack of exposure to these factors is thought to prevent proper education and training of the immune system. Increased industrialization and urbanization have brought about increases in organic and inorganic pollutants. In addition, Caesarian birth, birth order, increased use of soaps and detergents, tobacco smoke exposure and psychosomatic factors are other factors that have been associated with increased rate of allergic diseases. Here, we review current knowledge on the environmental factors that have been shown to affect the development of allergic diseases and the recent developments in the field.
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Affiliation(s)
- Shifaa Suhayl Alkotob
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Cade Cannedy
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Katharina Harter
- Chair and Institute of Environmental Medicine UNIKA‐TTechnical University of Munich and Helmholtz Zentrum München Augsburg Germany
| | - Hesam Movassagh
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Bibek Paudel
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Mary Prunicki
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Vanitha Sampath
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Tamara Schikowski
- IUF‐Leibniz Institute for Environmental Medicine Duesseldorf Germany
| | - Eric Smith
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Qi Zhao
- IUF‐Leibniz Institute for Environmental Medicine Duesseldorf Germany
| | - Claudia Traidl‐Hoffmann
- Chair and Institute of Environmental Medicine UNIKA‐TTechnical University of Munich and Helmholtz Zentrum München Augsburg Germany
- CK‐CARE Christine Kühne Center for Allergy Research and Education Davos Switzerland
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
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99997
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Xu X, Chen Y, Tan B, Wang D, Yuan Z, Wang F. Circular RNA circ_0011269 sponges miR-122 to regulate RUNX2 expression and promotes osteoporosis progression. J Cell Biochem 2020; 121:4819-4826. [PMID: 32619044 DOI: 10.1002/jcb.29709] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/12/2020] [Indexed: 01/20/2023]
Abstract
Circular RNAs (circRNAs) are a novel class of noncoding RNAs that are widely expressed in human disease. However, circRNAs expression profile and potential mechanism in osteoporosis pathogenesis remain to be further studied. In the present study, a total of 69 circRNAs were identified to be abnormally expressed in osteoporosis patient samples by microarray and bioinformatics analyses. We found that circ_0011269 was notably downregulated in osteoporosis (fold change, 3.94). By means of miRanda algorithm, we constructed the interaction network of circ_0011269-miRNAs in osteoporosis based on target binding and miR-122 was enrolled in the network. Dual-luciferase reporter assay verified the target relationship of miR-122 and circ_0011269/RUNX2. The expression of circ_0011269 and RUNX2 were gradually increased during osteogenic differentiation while miR-122 exhibited a decreased expression. Moreover, overexpression of circ_0011269 could promote RUNX2 expression and inhibit osteoporosis. In summary, this study found that circ_0011269 sponges miR-122 to regulate RUNX2 expression and promotes osteoporosis progression.
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Affiliation(s)
- Xiqiang Xu
- Department of Spine Surgery, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - Yuan Chen
- Department of Orthopedic Surgery, The 5th People's Hospital of Ji'nan, Jinan, Shandong, China
| | - Bingyi Tan
- Department of Spine Surgery, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - Dachuan Wang
- Department of Spine Surgery, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - Zenong Yuan
- Department of Spine Surgery, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - Feng Wang
- Department of Spine Surgery, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
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99998
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Jiang M, He Y, Chen X, Zhang X, Guo Y, Yang S, Huang J, Traw MB. CRISPR-based assessment of genomic structure in the conserved SQUAMOSA promoter-binding-like gene clusters in rice. Plant J 2020; 104:1301-1314. [PMID: 32996244 DOI: 10.1111/tpj.15001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/14/2020] [Accepted: 09/03/2020] [Indexed: 05/07/2023]
Abstract
Although SQUAMOSA promoter-binding-like (SPL) transcription factors are important regulators of development in rice (Oryza sativa), prior assessments of the SPL family have been limited to single genes. A functional comparison across the full gene family in standardized genetic backgrounds has not been reported previously. Here, we demonstrate that the SPL gene family in rice is enriched due to the most recent whole genome duplication (WGD). Notably, 10 of 19 rice SPL genes (52%) cluster in four units that have persisted for at least 50 million years. We show that SPL gene grouping and retention following WGD is widespread in angiosperms, suggesting the conservatism and importance of this gene arrangement. We used Cas9 editing to generate transformation lines for all 19 SPL genes in a common set of backgrounds, and found that knockouts of 14 SPL genes exhibited defects in plant height, 10 exhibited defects in panicle size, and nine had altered grain lengths. We observed subfunctionalization of genes in the paleoduplicated pairs, but little evidence of neofunctionalization. Expression of OsSPL3 was negatively correlated with that of its closest neighbor in its synteny group, OsSPL4, and its sister paired gene, OsSPL12, in the opposing group. Nucleotide diversity was lower in eight of the nine singleton genes in domesticated rice, relative to wild rice, whereas the reverse was true for the paired genes. Together, these results provide functional information on eight previously unexamined OsSPL family members and suggest that paleoduplicate pair redundancy benefits plant survival and innovation.
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Affiliation(s)
- Mengmeng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ying He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaonan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yanru Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ju Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - M Brian Traw
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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99999
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Miller ME, Nazareno ES, Rottschaefer SM, Riddle J, Dos Santos Pereira D, Li F, Nguyen-Phuc H, Henningsen EC, Persoons A, Saunders DGO, Stukenbrock E, Dodds PN, Kianian SF, Figueroa M. Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci. PLoS Genet 2020; 16:e1009291. [PMID: 33370783 PMCID: PMC7793281 DOI: 10.1371/journal.pgen.1009291] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 01/08/2021] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
Pathogen populations are expected to evolve virulence traits in response to resistance deployed in agricultural settings. However, few temporal datasets have been available to characterize this process at the population level. Here, we examined two temporally separated populations of Puccinia coronata f. sp. avenae (Pca), which causes crown rust disease in oat (Avena sativa) sampled from 1990 to 2015. We show that a substantial increase in virulence occurred from 1990 to 2015 and this was associated with a genetic differentiation between populations detected by genome-wide sequencing. We found strong evidence for genetic recombination in these populations, showing the importance of the alternate host in generating genotypic variation through sexual reproduction. However, asexual expansion of some clonal lineages was also observed within years. Genome-wide association analysis identified seven Avr loci associated with virulence towards fifteen Pc resistance genes in oat and suggests that some groups of Pc genes recognize the same pathogen effectors. The temporal shift in virulence patterns in the Pca populations between 1990 and 2015 is associated with changes in allele frequency in these genomic regions. Nucleotide diversity patterns at a single Avr locus corresponding to Pc38, Pc39, Pc55, Pc63, Pc70, and Pc71 showed evidence of a selective sweep associated with the shift to virulence towards these resistance genes in all 2015 collected isolates.
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Affiliation(s)
- Marisa E. Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eric S. Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Susan M. Rottschaefer
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Jakob Riddle
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, United States of America
| | - Danilo Dos Santos Pereira
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, Plon, Germany
- Christian-Albrechts University of Kiel, Kiel Germany
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Hoa Nguyen-Phuc
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eva C. Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Antoine Persoons
- INRA/Universite de Lorraine Interactions Abres/Microorganismes, Champenoux, France
| | | | - Eva Stukenbrock
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, Plon, Germany
- Christian-Albrechts University of Kiel, Kiel Germany
| | - Peter N. Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australia
| | - Shahryar F. Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, United States of America
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australia
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100000
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Abstract
Cell plasticity is important in development and tissue remodeling. Cells can sense physical and chemical cues from their local microenvironment and transduce the signals into the nucleus to regulate the epigenetic state and gene expression, resulting in a change in cell phenotype. In this review, we highlight the role of mechanical cues in regulating stem cell differentiation and cell reprogramming through the modulation of histone modifications. The effects of various mechanical cues, including matrix stiffness, mechanical stretch, and shear stress, on cell fate during tissue regeneration and remodeling will be discussed. Taken together, recent work demonstrates that the alterations in histone modifications by mechanical stimuli can facilitate epigenetic changes during cell phenotypic switching, which has potential applications in the development of biomaterials and bioreactors for cell engineering.
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Affiliation(s)
- Yang Song
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jennifer Soto
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Song Li
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
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