1
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Jenkins D. How do stochastic processes and genetic threshold effects explain incomplete penetrance and inform causal disease mechanisms? Philos Trans R Soc Lond B Biol Sci 2024; 379:20230045. [PMID: 38432317 PMCID: PMC10909503 DOI: 10.1098/rstb.2023.0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/16/2024] [Indexed: 03/05/2024] Open
Abstract
Incomplete penetrance is the rule rather than the exception in Mendelian disease. In syndromic monogenic disorders, phenotypic variability can be viewed as the combination of incomplete penetrance for each of multiple independent clinical features. Within genetically identical individuals, such as isogenic model organisms, stochastic variation at molecular and cellular levels is the primary cause of incomplete penetrance according to a genetic threshold model. By defining specific probability distributions of causal biological readouts and genetic liability values, stochasticity and incomplete penetrance provide information about threshold values in biological systems. Ascertainment of threshold values has been achieved by simultaneous scoring of relatively simple phenotypes and quantitation of molecular readouts at the level of single cells. However, this is much more challenging for complex morphological phenotypes using experimental and reductionist approaches alone, where cause and effect are separated temporally and across multiple biological modes and scales. Here I consider how causal inference, which integrates observational data with high confidence causal models, might be used to quantify the relative contribution of different sources of stochastic variation to phenotypic diversity. Collectively, these approaches could inform disease mechanisms, improve predictions of clinical outcomes and prioritize gene therapy targets across modes and scales of gene function. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Dagan Jenkins
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
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2
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Prince S. Gene-environment interaction: why genetic enhancement might never be distributed fairly. JOURNAL OF MEDICAL ETHICS 2024; 50:272-277. [PMID: 37268408 DOI: 10.1136/jme-2023-109101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/19/2023] [Indexed: 06/04/2023]
Abstract
Ethical debates around genetic enhancement tend to include an argument that the technology will eventually be fairly accessible once available. That we can fairly distribute genetic enhancement has become a moral defence of genetic enhancement. Two distribution solutions are argued for, the first being equal distribution. Equality of access is generally believed to be the fairest and most just method of distribution. Second, equitable distribution: providing genetic enhancements to reduce social inequalities. In this paper, I make two claims. I first argue that the very assumption that genetic enhancements can be distributed fairly is problematic when considering our understanding of gene-environment interactions, for example, epigenetics. I then argue that arguments that genetic enhancements are permissible because the intended benefits can be distributed fairly as intended are misinformed. My first claim rests on the assertion that genetic enhancements do not enhance traits in a vacuum; genes are dependent on conducive environments for expression. If society cannot guarantee fair environments, then any benefit conferred from being genetically enhanced will be undermined. Thus, any argument that the distribution of genetic enhancements will be fair and that the technology is therefore morally permissible, is mistaken.
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Affiliation(s)
- Sinead Prince
- Faculty of Business and Law, Queensland University of Technology, Brisbane, Queensland, Australia
- Faculty of Business and Law, Queensland University of Technology, Brisbane, Queensland, Australia
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3
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Kamzolas O, Papazoglou AS, Gemousakakis E, Moysidis DV, Kyriakoulis KG, Brilakis ES, Milkas A. Concomitant Coronary Artery Disease in Identical Twins: Case Report and Systematic Literature Review. J Clin Med 2023; 12:5742. [PMID: 37685809 PMCID: PMC10489011 DOI: 10.3390/jcm12175742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Coronary artery disease (CAD) is multifactorial and strongly affected by genetic, epigenetic and environmental factors. Several studies have reported development of concomitant CAD in identical twins. We report a case in which a pair of Caucasian male monozygotic twins presented almost concomitantly with acute coronary syndrome (ACS) and had concordant coronary anatomy and identical site of occlusion. We performed a systematic literature review of PubMed, Web Of Science and Scopus databases from inception until 28 February 2023 of case reports/case series reporting the concomitant development of CAD in monozygotic twins. We found 25 eligible case reports with a total of 31 monozygotic twin pairs (including the case from our center) suffering from CAD and presenting (most of them simultaneously) with ACS (mean age of presentation: 45 ± 12 years, males: 81%). Coronary angiograms demonstrated lesion and anatomy concordance in 77% and 79% of the twin pairs, respectively. Screening for disease-related genetic mutations was performed in six twin pairs leading to the identification of five CAD-related genetic polymorphisms. This is the first systematic literature review of studies reporting identical twin pairs suffering from CAD. In summary, there is high concordance of coronary anatomy and clinical presentation between monozygotic twins. Future monozygotic twin studies-unbiased by age effects-can provide insights into CAD heritability being able to disentangle the traditional dyad of genetic and environmental factors and investigate the within-pair epigenetic drift.
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Affiliation(s)
| | | | | | | | | | - Emmanouil S Brilakis
- Center for Coronary Artery Disease, Minneapolis Heart Institute and Minneapolis Heart Institute Foundation, Abbott Northwestern, Minneapolis, MN 55407, USA
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Lee DY, Jeong JY, Lee SE, Lee JH, Moon JY, Jung SW, Lee SH, Kim YG. Discordant renal progression of Fabry disease in male monozygotic twins: a case report. Front Genet 2023; 14:1150822. [PMID: 37388940 PMCID: PMC10300636 DOI: 10.3389/fgene.2023.1150822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023] Open
Abstract
Background: Fabry disease (FD) is a rare X-linked lysosomal storage disease caused by mutations in the GLA gene that encodes α-galactosidase A (α-GAL). Clinical phenotypes tend to vary in monozygotic female twins because mutations are located on the X-chromosome, whereas similar phenotypes are found in male monozygotic twins. Here we report the case of male monozygotic twins with FD presenting with distinguishable renal phenotypes. Case: A 49-year-old male patient who visited the hospital with proteinuria 14 years prior was readmitted for the same issue. His monozygotic twin brother had started hemodialysis 6 months prior due to renal failure of unknown origin. The patient's renal function was within the normal range, while his spot urine protein-to-creatinine ratio was 557 mg/g. Echocardiography revealed left ventricular hypertrophy (LVH). The findings of a renal biopsy were consistent with FD. Genetic testing identified a c.656T>C mutation in the GLA gene, and α-GAL activity was significantly decreased. Genetic screening of his family clarified that his mother, older sister, twin brother, and his daughter had the same genetic mutations. The patient received enzyme replacement therapy 34 times. Subsequently, migalastat was initiated that continues today. Renal function and proteinuria remain stable, and the LVH has mildly improved. Conclusion: This is the first case of male monozygotic twins expressing different progressions of FD. Our findings demonstrate the possibility that environmental or epigenetic factors may critically influence genotype-phenotype discordance.
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Affiliation(s)
- Do-Yun Lee
- College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Jun-Yeong Jeong
- College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Seung-Eun Lee
- College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Jae-Hun Lee
- College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Ju-Young Moon
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Su Woong Jung
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Sang-Ho Lee
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Yang Gyun Kim
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
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5
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Smederevac S, Delgado-Cruzata L, Mitrović D, Dinić BM, Bravo TAT, Delgado M, Bugarski Ignjatović V, Sadiković S, Milovanović I, Vučinić N, Branovački B, Prinz M, Budimlija Z, Kušić‐Tišma J, Nikolašević Ž. Differences in MB-COMT DNA methylation in monozygotic twins on phenotypic indicators of impulsivity. Front Genet 2023; 13:1067276. [PMID: 36685886 PMCID: PMC9852709 DOI: 10.3389/fgene.2022.1067276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/28/2022] [Indexed: 01/09/2023] Open
Abstract
Epigenetic modifications of the membrane bound catechol-O-methyltransferase (MB-COMT) gene may affect the enzymatic degradation of dopamine, and consequently, human behavior. This study investigated the association between membrane bound catechol-O-methyltransferase DNA methylation (DNAm) differences in 92 monozygotic (MZ) twins with phenotypic manifestations of cognitive, behavioral, and personality indicators associated with reward-related behaviors and lack of control. We used pyrosequencing to determine DNAm of the regulatory region of membrane bound catechol-O-methyltransferase in saliva DNA. Results of intrapair differences in the percentage of membrane bound catechol-O-methyltransferase DNAm at each of five CpG sites show that there are associations between phenotypic indicators of lack of control and membrane bound catechol-O-methyltransferase DNAm differences on CpG1, CpG2 and CpG4, suggesting the common epigenetic patterns for personality traits, cognitive functions, and risk behaviors.
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Affiliation(s)
- Snežana Smederevac
- Department of Psychology, Faculty of Philosophy, University of Novi Sad, Novi Sad, Serbia,*Correspondence: Selka Sadiković, ; Snežana Smederevac,
| | | | - Dušanka Mitrović
- Department of Psychology, Faculty of Philosophy, University of Novi Sad, Novi Sad, Serbia
| | - Bojana M. Dinić
- Department of Psychology, Faculty of Philosophy, University of Novi Sad, Novi Sad, Serbia
| | | | - Maria Delgado
- Mount Holyoke College, South Hadley, MA, United States
| | | | - Selka Sadiković
- Department of Psychology, Faculty of Philosophy, University of Novi Sad, Novi Sad, Serbia,*Correspondence: Selka Sadiković, ; Snežana Smederevac,
| | - Ilija Milovanović
- Department of Psychology, Faculty of Philosophy, University of Novi Sad, Novi Sad, Serbia
| | - Nataša Vučinić
- Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | - Bojan Branovački
- Department of Psychology, Faculty of Philosophy, University of Novi Sad, Novi Sad, Serbia
| | - Mechthild Prinz
- John Jay College of Criminal Justice, New York, NY, United States
| | - Zoran Budimlija
- Department of Neurology, School of Medicine, New York University, New York City, NY, United States
| | - Jelena Kušić‐Tišma
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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6
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Ogbunugafor CB, Edge MD. Gattaca as a lens on contemporary genetics: marking 25 years into the film's "not-too-distant" future. Genetics 2022; 222:iyac142. [PMID: 36218390 PMCID: PMC9713434 DOI: 10.1093/genetics/iyac142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
The 1997 film Gattaca has emerged as a canonical pop culture reference used to discuss modern controversies in genetics and bioethics. It appeared in theaters a few years prior to the announcement of the "completion" of the human genome (2000), as the science of human genetics was developing a renewed sense of its social implications. The story is set in a near-future world in which parents can, with technological assistance, influence the genetic composition of their offspring on the basis of predicted life outcomes. The current moment-25 years after the film's release-offers an opportunity to reflect on where society currently stands with respect to the ideas explored in Gattaca. Here, we review and discuss several active areas of genetic research-genetic prediction, embryo selection, forensic genetics, and others-that interface directly with scenes and concepts in the film. On its silver anniversary, we argue that Gattaca remains an important reflection of society's expectations and fears with respect to the ways that genetic science has manifested in the real world. In accompanying supplemental material, we offer some thought questions to guide group discussions inside and outside of the classroom.
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Affiliation(s)
- C Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
- Vermont Complex Systems Center, Burlington, VT 05401, USA
| | - Michael D Edge
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
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7
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The emergence and development of behavioral individuality in clonal fish. Nat Commun 2022; 13:6419. [PMID: 36307437 PMCID: PMC9616841 DOI: 10.1038/s41467-022-34113-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/13/2022] [Indexed: 12/25/2022] Open
Abstract
Behavioral individuality is a ubiquitous phenomenon in animal populations, yet the origins and developmental trajectories of individuality, especially very early in life, are still a black box. Using a high-resolution tracking system, we mapped the behavioral trajectories of genetically identical fish (Poecilia formosa), separated immediately after birth into identical environments, over the first 10 weeks of their life at 3 s resolution. We find that (i) strong behavioral individuality is present at the very first day after birth, (ii) behavioral differences at day 1 of life predict behavior up to at least 10 weeks later, and (iii) patterns of individuality strengthen gradually over developmental time. Our results establish a null model for how behavioral individuality can develop in the absence of genetic and environmental variation and provide experimental evidence that later-in-life individuality can be strongly shaped by factors pre-dating birth like maternal provisioning, epigenetics and pre-birth developmental stochasticity.
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8
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Smyth LK, Balme GA, Tyzack-Pitman R, Bishop JM, Justin O’Riain M. Like mother like daughter: quantifying the relationship between relatedness and phenotypic similarity in leopard pelage patterns. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00308-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Smagin DA, Kovalenko IL, Galyamina AG, Belozertseva IV, Tamkovich NV, Baranov KO, Kudryavtseva NN. Chronic Lithium Treatment Affects Anxious Behaviors and theExpression of Serotonergic Genes in Midbrain Raphe Nuclei of Defeated Male Mice. Biomedicines 2021; 9:biomedicines9101293. [PMID: 34680410 PMCID: PMC8533389 DOI: 10.3390/biomedicines9101293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 01/07/2023] Open
Abstract
There is experimental evidence that chronic social defeat stress is accompanied by the development of an anxiety, development of a depression-like state, and downregulation of serotonergic genes in midbrain raphe nuclei of male mice. Our study was aimed at investigating the effects of chronic lithium chloride (LiCl) administration on anxiety behavior and the expression of serotonergic genes in midbrain raphe nuclei of the affected mice. A pronounced anxiety-like state in male mice was induced by chronic social defeat stress in daily agonistic interactions. After 6 days of this stress, defeated mice were chronically treated with saline or LiCl (100 mg/kg, i.p., 2 weeks) during the continuing agonistic interactions. Anxiety was assessed by behavioral tests. RT-PCR was used to determine Tph2, Htr1a, Htr5b, and Slc6a4 mRNA expression. The results revealed anxiolytic-like effects of LiCl on social communication in the partition test and anxiogenic-like effects in both elevated plus-maze and social interaction tests. Chronic LiCl treatment upregulated serotonergic genes in midbrain raphe nuclei. Thus, LiCl effects depend on the treatment mode, psycho-emotional state of the animal, and experimental context (tests). It is assumed that increased expression of serotonergic genes is accompanied by serotonergic system activation and, as a side effect, by higher anxiety.
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Affiliation(s)
- Dmitry A. Smagin
- FRC Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.A.S.); (I.L.K.); (A.G.G.)
| | - Irina L. Kovalenko
- FRC Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.A.S.); (I.L.K.); (A.G.G.)
| | - Anna G. Galyamina
- FRC Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.A.S.); (I.L.K.); (A.G.G.)
| | - Irina V. Belozertseva
- Valdman Institute of Pharmacology, First Pavlov State Medical University of St. Petersburg, 197022 St. Petersburg, Russia;
| | | | - Konstantin O. Baranov
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Natalia N. Kudryavtseva
- FRC Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.A.S.); (I.L.K.); (A.G.G.)
- Pavlov Institute of Physiology, Russian Academy of Sciences, 188680 St. Petersburg, Russia
- Head of Neuropathology Modeling Laboratory, Institute of Cytology and Genetics SB RAS, pr. Ac. Lavrentjev, 10, 630090 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-(383)-363-49-65
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10
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Wang X, Wei L, Yang J, Wang Y, Chen S, Yang K, Meng X, Zhang L. DNA methylation determines the regulation of pregnane X receptor on CYP3A4 expression. Clin Exp Pharmacol Physiol 2021; 48:250-259. [PMID: 33048369 DOI: 10.1111/1440-1681.13420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/22/2020] [Accepted: 10/07/2020] [Indexed: 11/30/2022]
Abstract
The expression and activity of CYP3A4 vary among individuals. With the development of epigenetics, it is now possible to elucidate interindividual differences in drug-metabolizing enzymes. Here, we aimed to explore the potential relationship between DNA methylation and CYP3A4 expression. We analyzed the effect of a DNA methylation inhibitor, 5-aza-2-deoxycytidine, on pregnane X receptor (PXR) and CYP3A4 expression in HepG2 cells. In addition, pCpGL-CYP3A4-promoter and pCpGL-CYP3A4-enhancer plus promoter plasmids were constructed, methylated, and transfected. We found that treatment with 5-aza-2-deoxycytidine significantly increased the expression of PXR and CYP3A4 in a concentration- and time-dependent manner. In addition, CYP3A4 expression was significantly enhanced by overexpressing PXR via transfection of pSG5-PXR plasmids. Methylation of CYP3A4 enhancer inhibited CYP3A4 transcriptional activity mediated through PXR and inhibited the binding of PXR and CYP3A4 promoter. We also observed that when the promoter and enhancer of CYP3A4 were methylated, CYP3A4 expression did not increase after treatment with rifampicin. In conclusion, the investigation demonstrates that DNA methylation of CYP3A4 enhancer significantly inhibits CYP3A4 expression, mediated through PXR, which is not influenced by rifampicin.
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Affiliation(s)
- Xiaofei Wang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Luman Wei
- Department of Pharmacy, Zhengzhou People's Hospital, Zhengzhou, China
| | - Jingke Yang
- Laboratory of Cardiovascular Disease and Drug Research, The 7th People's Hospital of Zhengzhou, Zhengzhou, China
| | - Yiting Wang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Shitong Chen
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Kun Yang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Xiangguang Meng
- Laboratory of Cardiovascular Disease and Drug Research, The 7th People's Hospital of Zhengzhou, Zhengzhou, China
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
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11
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Mendenhall AR, Martin GM, Kaeberlein M, Anderson RM. Cell-to-cell variation in gene expression and the aging process. GeroScience 2021; 43:181-196. [PMID: 33595768 PMCID: PMC8050212 DOI: 10.1007/s11357-021-00339-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
There is tremendous variation in biological traits, and much of it is not accounted for by variation in DNA sequence, including human diseases and lifespan. Emerging evidence points to differences in the execution of the genetic program as a key source of variation, be it stochastic variation or programmed variation. Here we discuss variation in gene expression as an intrinsic property and how it could contribute to variation in traits, including the rate of aging. The review is divided into sections describing the historical context and evidence to date for nongenetic variation, the different approaches that may be used to detect nongenetic variation, and recent findings showing that the amount of variation in gene expression can be both genetically programmed and epigenetically controlled. Finally, we present evidence that changes in cell-to-cell variation in gene expression emerge as part of the aging process and may be linked to disease vulnerability as a function of age. These emerging concepts are likely to be important across the spectrum of biomedical research and may well underpin what we understand as biological aging.
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Affiliation(s)
- Alexander R Mendenhall
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA.
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA.
| | - George M Martin
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA
| | - Rozalyn M Anderson
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin and Geriatric Research Education and Clinical Center, William S Middleton Memorial Veterans Hospital, Madison, WI, USA.
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12
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Pozo MI, Hunt BJ, Van Kemenade G, Guerra-Sanz JM, Wäckers F, Mallon EB, Jacquemyn H. The effect of DNA methylation on bumblebee colony development. BMC Genomics 2021; 22:73. [PMID: 33482723 PMCID: PMC7821684 DOI: 10.1186/s12864-021-07371-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Although around 1% of cytosines in bees' genomes are known to be methylated, less is known about methylation's effect on bee behavior and fitness. Chemically altered DNA methylation levels have shown clear changes in the dominance and reproductive behavior of workers in queen-less colonies, but the global effect of DNA methylation on caste determination and colony development remains unclear, mainly because of difficulties in controlling for genetic differences among experimental subjects in the parental line. Here, we investigated the effect of the methylation altering agent decitabine on the developmental rate of full bumblebee colonies. Whole genome bisulfite sequencing was used to assess differences in methylation status. RESULTS Our results showed fewer methylated loci in the control group. A total of 22 CpG loci were identified as significantly differentially methylated between treated and control workers with a change in methylation levels of 10% or more. Loci that were methylated differentially between groups participated in pathways including neuron function, oocyte regulation and metabolic processes. Treated colonies tended to develop faster, and therefore more workers were found at a given developmental stage. However, male production followed the opposite trend and it tended to be higher in control colonies. CONCLUSION Overall, our results indicate that altered methylation patterns resulted in an improved cooperation between workers, while there were no signs of abnormal worker dominance or caste determination.
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Affiliation(s)
- María I Pozo
- KU Leuven, Biology Department, Plant Population and Conservation Biology, B-3001, Heverlee, Belgium.
| | - Benjamin J Hunt
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | | | | | - Felix Wäckers
- Biobest Group, Research and Development, B-2260, Westerlo, Belgium
| | - Eamonn B Mallon
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Hans Jacquemyn
- KU Leuven, Biology Department, Plant Population and Conservation Biology, B-3001, Heverlee, Belgium
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13
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Reynolds KJ, Turner JC, Branscombe NR, Mavor KI, Bizumic B, Subašić E. Further Integration of Social Psychology and Personality Psychology: Choice or Necessity? EUROPEAN JOURNAL OF PERSONALITY 2021. [DOI: 10.1002/per.784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - John C. Turner
- Department of Psychology, The Australian National University, Canberra, Australia
| | | | - Kenneth I. Mavor
- Department of Psychology, The Australian National University, Canberra, Australia
| | - Boris Bizumic
- Department of Psychology, The Australian National University, Canberra, Australia
| | - Emina Subašić
- Department of Psychology, The Australian National University, Canberra, Australia
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14
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Erdogan OS, Tuncer SB, Kilic S, Odemis DA, Turkcan GK, Celik B, Avsar M, Yazici H. Genome-wide methylation profiles in monozygotic twins with discordance for ovarian carcinoma. Oncol Lett 2020; 20:357. [PMID: 33133257 PMCID: PMC7590432 DOI: 10.3892/ol.2020.12221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/19/2020] [Indexed: 12/24/2022] Open
Abstract
Ovarian cancer is a disease that is generally diagnosed at an advanced stage, and has poor survival. Monozygotic (MZ) twins are considered to be good research models for investigating the epigenetic changes associated with diseases. In the present study, the involvement of epigenetic mechanisms in ovarian cancer etiology were evaluated using the MZ twin model. Whole-genome methylation patterns were investigated in a BRCA1 gene mutation-carrying family comprising MZ twins, only one of whom had ovarian cancer, and other healthy siblings. Whole-genome methylation patterns were assessed in peripheral blood DNA using Infinium MethylationEPIC BeadChips on an Illumina iScan device. The hypermethylated and hypomethylated genes were detected between cases and controls in four different comparison groups in order to evaluate the differences in methylation levels according to cancer diagnosis and BRCA mutation status. The obtained results showed that the differential methylations in 12 different genes, namely PR/SET domain 6, cytochrome B5 reductase 4, ZNF714, OR52M1, SEMA4D, CHD1L, CAPZB, clustered mitochondria homolog, RB-binding protein 7, chromatin repair factor, ankyrin repeat domain 23, RIB43A domain with coiled-coils 1 and C6orf227, were associated with ovarian cancer. Biological functional analysis of the genes detected in the study using the PANTHER classification system revealed that they have roles in biological processes including ‘biologic adhesion’, ‘regulation’, ‘cellular components organization’, ‘biogenesis’, ‘immune system functioning’, ‘metabolic functioning’ and ‘localization’. Overall, the present study suggested that epigenetic differences, such as methylation status, could be used as a non-invasive biological markers for the early diagnosis and follow-up of ovarian cancer.
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Affiliation(s)
- Ozge Sukruoglu Erdogan
- Department of Basic Oncology, Cancer Genetics Division, Institute of Oncology, Istanbul University, Istanbul 34093, Turkey
| | - Seref Bugra Tuncer
- Department of Basic Oncology, Cancer Genetics Division, Institute of Oncology, Istanbul University, Istanbul 34093, Turkey
| | - Seda Kilic
- Department of Basic Oncology, Cancer Genetics Division, Institute of Oncology, Istanbul University, Istanbul 34093, Turkey
| | - Demet Akdeniz Odemis
- Department of Basic Oncology, Cancer Genetics Division, Institute of Oncology, Istanbul University, Istanbul 34093, Turkey
| | - Gozde Kuru Turkcan
- Department of Basic Oncology, Cancer Genetics Division, Institute of Oncology, Istanbul University, Istanbul 34093, Turkey
| | - Betul Celik
- Department of Basic Oncology, Cancer Genetics Division, Institute of Oncology, Istanbul University, Istanbul 34093, Turkey
| | - Mukaddes Avsar
- Department of Basic Oncology, Cancer Genetics Division, Institute of Oncology, Istanbul University, Istanbul 34093, Turkey
| | - Hulya Yazici
- Department of Basic Oncology, Cancer Genetics Division, Institute of Oncology, Istanbul University, Istanbul 34093, Turkey
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15
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Heo GE, Xie Q, Song M, Lee JH. Combining entity co-occurrence with specialized word embeddings to measure entity relation in Alzheimer's disease. BMC Med Inform Decis Mak 2019; 19:240. [PMID: 31801521 PMCID: PMC6894106 DOI: 10.1186/s12911-019-0934-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Background Extracting useful information from biomedical literature plays an important role in the development of modern medicine. In natural language processing, there have been rigorous attempts to find meaningful relationships between entities automatically by co-occurrence-based methods. It has been increasingly important to understand whether relationships exist, and if so how strong, between any two entities extracted from a large number of texts. One of the defining methods is to measure semantic similarity and relatedness between two entities. Methods We propose a hybrid ranking method that combines a co-occurrence approach considering both direct and indirect entity pair relationship with specialized word embeddings for measuring the relatedness of two entities. Results We evaluate the proposed ranking method comparatively with other well-known methods such as co-occurrence, Word2Vec, COALS (Correlated Occurrence Analog to Lexical Semantics), and random indexing by calculating top-ranked entities related to Alzheimer’s disease. In addition, we analyze gene, pathway, and gene–phenotype relationships. Overall, the proposed method tends to find more hidden relationships than the other methods. Conclusion Our proposed method is able to select more useful related entities that not only highly co-occur but also have more indirect relations for the target entity. In pathway analysis, our proposed method shows superior performance at identifying (functional) cross clustering and higher-level pathways. Our proposed method, resulting from phenotype analysis, has an advantage in identifying the common genotype relating to phenotypes from biological literature.
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Affiliation(s)
- Go Eun Heo
- Department of Library and Information Science, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Qing Xie
- Department of Library and Information Science, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Min Song
- Department of Library and Information Science, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Jeong-Hoon Lee
- Department of Creative IT Engineering, POSTECH, 77 Cheongam-ro Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
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16
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Popescu C. Monozygotic Twins Discordant for Kennedy Disease: A Case Report. J Clin Neuromuscul Dis 2019; 21:112-116. [PMID: 31743255 DOI: 10.1097/cnd.0000000000000266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Spinal and bulbar muscular atrophy or Kennedy disease (KD) is an X-linked recessive disorder caused by a pathogenic CAG expansion in the first exon of the androgen receptor. Proximal muscle atrophy, weakness, contraction fasciculations, bulbar involvement, and sensory disturbances are part of the clinical picture of KD. We report the unusual genetic and phenotypic expression in 2 monozygotic twins. Genetic analysis has shown abnormal expansion of CAG repeat in the first exon of the androgen receptor gene on chromosome X different between the twin brothers (44, respectively, 46) but with large phenotypical differences including onset age, evolution, and clinical features. Disease began at age 31 for the first brother, respectively, and at 56 years for the second one and consisted of muscle wasting and progressive impairment of walking. In addition, the second brother did not manifest bulbar involvement 3 years after clinical onset and has more sensory features. Besides classical EMG testing, we evaluate sensory participation in spinal and bulbar muscular atrophy with sudoscan device and confirmed the sensory deficit. We discussed epigenetic factors potentially involved in KD that could play a role in the phenotypical differences. To the best of our knowledge, this is the first case describing CAG trinucleotide repeats in monozygotic twins and also the first sudoscan diagnostic of sensory disturbances in Kennedy syndrome.
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17
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Affiliation(s)
- Arturas Petronis
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Viviane Labrie
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
- Division of Psychiatry and Behavioral Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
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18
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Multilevel fine-scale diversity challenges the 'cryptic species' concept. Sci Rep 2019; 9:6732. [PMID: 31043629 PMCID: PMC6494890 DOI: 10.1038/s41598-019-42297-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 03/29/2019] [Indexed: 01/08/2023] Open
Abstract
‘Cryptic’ species are an emerging biological problem that is broadly discussed in the present study. Recently, a cryptic species definition was suggested for those species which manifest low morphological, but considerable genetic, disparity. As a case study we present unique material from a charismatic group of nudibranch molluscs of the genus Trinchesia from European waters to reveal three new species and demonstrate that they show a dual nature: on one hand, they can be considered a ‘cryptic’ species complex due to their overall similarity, but on the other hand, stable morphological differences as well as molecular differences are demonstrated for every species in that complex. Thus, this species complex can equally be named ‘cryptic’, ‘pseudocryptic’ or ‘non-cryptic’. We also present evidence for an extremely rapid speciation rate in this species complex and link the species problem with epigenetics. Available metazoan-wide data, which are broadly discussed in the present study, show the unsuitability of a ‘cryptic’ species concept because the degree of crypticity represents a continuum when a finer multilevel morphological and molecular scale is applied to uncover more narrowly defined species making the ‘cryptic’ addition to ‘species’ redundant. Morphological and molecular methods should be applied in concordance to form a fine-scale multilevel taxonomic framework, and not necessarily implying only an a posteriori transformation of exclusively molecular-based ‘cryptic’ species into morphologically-defined ‘pseudocryptic’ ones. Implications of the present study have importance for many fields, including conservation biology and fine-scale biodiversity assessments.
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19
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Lynch C, Fleming R. A review of direct polymerase chain reaction of DNA and RNA for forensic purposes. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/wfs2.1335] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Courtney Lynch
- Forensic Research and Development Team, Institute of Environmental Science and Research Ltd Auckland New Zealand
- School of Chemical Sciences University of Auckland Auckland New Zealand
| | - Rachel Fleming
- Forensic Research and Development Team, Institute of Environmental Science and Research Ltd Auckland New Zealand
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20
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Mukherjee K, Dubovskiy I, Grizanova E, Lehmann R, Vilcinskas A. Epigenetic mechanisms mediate the experimental evolution of resistance against parasitic fungi in the greater wax moth Galleria mellonella. Sci Rep 2019; 9:1626. [PMID: 30733453 PMCID: PMC6367475 DOI: 10.1038/s41598-018-36829-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/23/2018] [Indexed: 02/07/2023] Open
Abstract
Recent concepts in evolutionary biology suggest that epigenetic mechanisms can translate environmental selection pressures into heritable changes in phenotype. To determine whether experimental selection for a complex trait in insects involves epigenetic modifications, we carried out a generation-spanning experiment using larvae of the greater wax moth Galleria mellonella as a model host to investigate the role of epigenetics in the heritability of resistance against the parasitic fungus Metarhizium robertsii. We investigated differences in DNA methylation, histone acetylation and microRNA (miRNA) expression between an experimentally resistant population and an unselected, susceptible line, revealing that the survival of G. mellonella larvae infected with M. robertsii correlates with tissue-specific changes in DNA methylation and histone modification and the modulation of genes encoding the corresponding enzymes. We also identified miRNAs differentially expressed between resistant and susceptible larvae and showed that these regulatory molecules target genes encoding proteinases and proteinase inhibitors, as well as genes related to cuticle composition, innate immunity and metabolism. These results support our hypothesis that epigenetic mechanisms facilitate, at least in part, the heritable manifestation of parasite resistance in insects. The reciprocal adaptations underlying host–parasite coevolution therefore extend beyond the genetic level to encompass epigenetic modifications.
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Affiliation(s)
- Krishnendu Mukherjee
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Str. 2, 35394, Giessen, Germany
| | - Ivan Dubovskiy
- Novosibirsk State Agrarian University, Dobrolubova 160, 630039, Novosibirsk, Russia
| | - Ekaterina Grizanova
- Novosibirsk State Agrarian University, Dobrolubova 160, 630039, Novosibirsk, Russia
| | - Rüdiger Lehmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Str. 2, 35394, Giessen, Germany
| | - Andreas Vilcinskas
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Str. 2, 35394, Giessen, Germany. .,Institute for Insect Biotechnology, Justus-Liebig University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
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21
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Rugiu L, Manninen I, Rothäusler E, Jormalainen V. Tolerance to climate change of the clonally reproducing endemic Baltic seaweed, Fucus radicans: is phenotypic plasticity enough? JOURNAL OF PHYCOLOGY 2018; 54:888-898. [PMID: 30315649 DOI: 10.1111/jpy.12796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 09/21/2018] [Indexed: 06/08/2023]
Abstract
To predict the effects of climate change, we first need information on both the current tolerance ranges of species and their future adaptive potential. Adaptive responses may originate either in genetic variation or in phenotypic plasticity, but the relative importance of these factors is poorly understood. Here, we tested the tolerance of Fucus radicans to the combination of hyposalinity and warming projected by climate models for 2070-2099. We measured the growth and survival responses of thalli in both current and future conditions, focusing on variations in tolerance among and within different clonal lineages. Survival was 32% lower in future than in current conditions, but the weight and length of the thalli which survived was respectively 267% and 178% higher when exposed to future conditions. The relatively high tolerance to the future conditions suggests that F. radicans is likely to persist in its current distributional range, which is limited to the Gulf of Bothia and Estonian coast in the Baltic Sea. Furthermore, this species may be able to expand its distribution southward and replace its congener F. vesiculosus, which, in previous studies, has not tolerated the future conditions as well. In addition, we discovered variation in tolerance to future conditions within one of the clonal lineages, which have been hitherto presumed to lack adaptive variation. The discovery of intra-clonal phenotypic plasticity means that this alga has the potential for adaptive responses to climate change, which may be the key to the future persistence of F. radicans in the Baltic Sea.
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Affiliation(s)
- Luca Rugiu
- Section of Ecology, Department of Biology, University of Turku, FIN-20014, Turku, Finland
| | - Iita Manninen
- Section of Ecology, Department of Biology, University of Turku, FIN-20014, Turku, Finland
| | - Eva Rothäusler
- Section of Ecology, Department of Biology, University of Turku, FIN-20014, Turku, Finland
| | - Veijo Jormalainen
- Section of Ecology, Department of Biology, University of Turku, FIN-20014, Turku, Finland
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22
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Thomson CE, Winney IS, Salles OC, Pujol B. A guide to using a multiple-matrix animal model to disentangle genetic and nongenetic causes of phenotypic variance. PLoS One 2018; 13:e0197720. [PMID: 30312317 PMCID: PMC6193571 DOI: 10.1371/journal.pone.0197720] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 09/19/2018] [Indexed: 11/19/2022] Open
Abstract
Non-genetic influences on phenotypic traits can affect our interpretation of genetic variance and the evolutionary potential of populations to respond to selection, with consequences for our ability to predict the outcomes of selection. Long-term population surveys and experiments have shown that quantitative genetic estimates are influenced by nongenetic effects, including shared environmental effects, epigenetic effects, and social interactions. Recent developments to the "animal model" of quantitative genetics can now allow us to calculate precise individual-based measures of non-genetic phenotypic variance. These models can be applied to a much broader range of contexts and data types than used previously, with the potential to greatly expand our understanding of nongenetic effects on evolutionary potential. Here, we provide the first practical guide for researchers interested in distinguishing between genetic and nongenetic causes of phenotypic variation in the animal model. The methods use matrices describing individual similarity in nongenetic effects, analogous to the additive genetic relatedness matrix. In a simulation of various phenotypic traits, accounting for environmental, epigenetic, or cultural resemblance between individuals reduced estimates of additive genetic variance, changing the interpretation of evolutionary potential. These variances were estimable for both direct and parental nongenetic variances. Our tutorial outlines an easy way to account for these effects in both wild and experimental populations. These models have the potential to add to our understanding of the effects of genetic and nongenetic effects on evolutionary potential. This should be of interest both to those studying heritability, and those who wish to understand nongenetic variance.
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Affiliation(s)
- Caroline E. Thomson
- Laboratoire Evolution & Diversité Biologique (EDB UMR 5174), Université Fédérale Toulouse, Midi-Pyrénées, CNRS, ENSFEA, IRD, UPS, France
| | - Isabel S. Winney
- Laboratoire Evolution & Diversité Biologique (EDB UMR 5174), Université Fédérale Toulouse, Midi-Pyrénées, CNRS, ENSFEA, IRD, UPS, France
| | - Océane C. Salles
- Laboratoire Evolution & Diversité Biologique (EDB UMR 5174), Université Fédérale Toulouse, Midi-Pyrénées, CNRS, ENSFEA, IRD, UPS, France
| | - Benoit Pujol
- Laboratoire Evolution & Diversité Biologique (EDB UMR 5174), Université Fédérale Toulouse, Midi-Pyrénées, CNRS, ENSFEA, IRD, UPS, France
- Laboratoire d’Excellence “CORAIL”, Perpignan, France
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23
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Jones KS, Weisrock DW. Genomic data reject the hypothesis of sympatric ecological speciation in a clade of Desmognathus salamanders. Evolution 2018; 72:2378-2393. [PMID: 30246244 DOI: 10.1111/evo.13606] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/05/2018] [Indexed: 12/22/2022]
Abstract
Closely related taxa with dissimilar morphologies are often considered to have diverged via natural selection favoring different phenotypes. However, some studies have found these scenarios to be paired with limited or no genetic differentiation. Desmognathus quadramaculatus and D. marmoratus are sympatric salamander species thought to represent a case of ecological speciation based on distinct morphologies, but the results of previous studies have not resolved corresponding patterns of lineage divergence. Here, we use genome-wide data to test this hypothesis of ecological speciation. Population structure analyses partitioned individuals geographically, but not morphologically, into two adjacent regions of western North Carolina: Pisgah and Nantahala. Phylogenetic analyses confirmed the nominal species are nonmonophyletic and resolved deep divergence between the two geographic clusters. Model-testing overwhelmingly supported the hypothesis that lineage divergence followed geography. Finally, ecological niche modeling showed that Pisgah and Nantahala individuals occupy different climatic niches, and geographic boundaries for the two lineages correspond to differences in precipitation regimes across southern Appalachia. Overall, we reject the previous hypothesis of ecological speciation based on microhabitat partitioning. Instead, our results suggest that there are two cryptic lineages, each containing the same pair of morphotypes.
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Affiliation(s)
- Kara S Jones
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506
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24
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Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation. Proc Natl Acad Sci U S A 2018; 115:E9145-E9152. [PMID: 30201727 PMCID: PMC6166847 DOI: 10.1073/pnas.1805371115] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
While clonally propagated individuals should share identical genomes, there is often substantial phenotypic variation among them. Both genetic and epigenetic modifications induced during regeneration have been associated with this phenomenon. Here we investigated the fate of the epigenome after asexual propagation by generating clonal individuals from differentiated somatic cells through the manipulation of a zygotic transcription factor. We found that phenotypic novelty in clonal progeny was linked to epigenetic imprints that reflect the organ used for regeneration. Some of these organ-specific imprints can be maintained during the cloning process and subsequent rounds of meiosis. Our findings are fundamental for understanding the significance of epigenetic variability arising from asexual reproduction and have significant implications for future biotechnological applications. Plants differ from animals in their capability to easily regenerate fertile adult individuals from terminally differentiated cells. This unique developmental plasticity is commonly observed in nature, where many species can reproduce asexually through the ectopic initiation of organogenic or embryogenic developmental programs. While organ-specific epigenetic marks are not passed on during sexual reproduction, the fate of epigenetic marks during asexual reproduction and the implications for clonal progeny remain unclear. Here we report that organ-specific epigenetic imprints in Arabidopsis thaliana can be partially maintained during asexual propagation from somatic cells in which a zygotic program is artificially induced. The altered marks are inherited even over multiple rounds of sexual reproduction, becoming fixed in hybrids and resulting in heritable molecular and physiological phenotypes that depend on the identity of the founder tissue. Consequently, clonal plants display distinct interactions with beneficial and pathogenic microorganisms. Our results demonstrate how novel phenotypic variation in plants can be unlocked through altered inheritance of epigenetic marks upon asexual propagation.
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25
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Takahashi M, Hosomichi K, Yamaguchi T, Nagahama R, Yoshida H, Marazita ML, Weinberg SM, Maki K, Tajima A. Exploration of genetic factors determining cleft side in a pair of monozygotic twins with mirror-image cleft lip and palate using whole-genome sequencing and comparison of craniofacial morphology. Arch Oral Biol 2018; 96:33-38. [PMID: 30172943 DOI: 10.1016/j.archoralbio.2018.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 08/15/2018] [Accepted: 08/17/2018] [Indexed: 12/15/2022]
Abstract
OBJECTIVE The aim of the present study is to explore genetic factors determining difference of cleft side using whole-genome sequencing and evaluation of craniofacial morphology using cephalometric analysis between Japanese monozygotic (MZ) twins with mirror-image cleft lip and palate (CLP). DESIGN We selected a Japanese MZ twin pair (MZ-A and MZ-B) affected with unilateral CLP who are discordant for cleft side (left/right) and conducted whole-genome sequencing to identify genetic factors determining cleft side. Moreover, we compared their craniofacial morphologies using cephalograms. RESULTS Whole-genome sequencing results suggested that no discordant DNA variants were found between MZ-A and MZ-B. The comparison of craniofacial morphology between the MZ twins revealed that MZ-B had maxillary deficiency and slightly more mandibular protrusion than MZ-A. CONCLUSIONS It is indicated that environmental factors might be a critical factor that influences the determination of difference of cleft side in orofacial clefts. In addition, we found some differences in craniofacial morphology between MZ-A and MZ-B. Our findings suggest that various environmental factors, such as epigenetics, might be a critical factor that influences the determination of difference of cleft side in CLP rather than inherited genetic factors.
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Affiliation(s)
- Masahiro Takahashi
- Department of Orthodontics, School of Dentistry, Showa University, Tokyo, Japan.
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Tetsutaro Yamaguchi
- Department of Orthodontics, School of Dentistry, Showa University, Tokyo, Japan; Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ryo Nagahama
- Department of Orthodontics, School of Dentistry, Showa University, Tokyo, Japan
| | - Hiroshi Yoshida
- Department of Orthodontics, School of Dentistry, Showa University, Tokyo, Japan
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA; Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Koutaro Maki
- Department of Orthodontics, School of Dentistry, Showa University, Tokyo, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
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26
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Epigenetic and Cellular Diversity in the Brain through Allele-Specific Effects. Trends Neurosci 2018; 41:925-937. [PMID: 30098802 DOI: 10.1016/j.tins.2018.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 01/18/2023]
Abstract
The benefits of diploidy are considered to involve masking partially recessive mutations and increasing genetic diversity. Here, we review new studies showing evidence for diverse allele-specific expression and epigenetic states in mammalian brain cells, which suggest that diploidy expands the landscape of gene regulatory and expression programs in cells. Allele-specific expression has been thought to be restricted to a few specific classes of genes. However, new studies show novel genomic imprinting effects that are brain-region-, cell-type- and age-dependent. In addition, novel forms of random monoallelic expression that impact many autosomal genes have been described in vitro and in vivo. We discuss the implications for understanding the benefits of diploidy, and the mechanisms shaping brain development, function, and disease.
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27
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Copy Number Variants and Exome Sequencing Analysis in Six Pairs of Chinese Monozygotic Twins Discordant for Congenital Heart Disease. Twin Res Hum Genet 2018; 20:521-532. [PMID: 29192580 PMCID: PMC5729853 DOI: 10.1017/thg.2017.57] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Congenital heart disease (CHD) is one of the most common birth defects. More than 200 susceptibility loci have been identified for CHDs, yet a large part of the genetic risk factors remain unexplained. Monozygotic (MZ) twins are thought to be completely genetically identical; however, discordant phenotypes have been found in MZ twins. Recent studies have demonstrated genetic differences between MZ twins. We aimed to test whether copy number variants (CNVs) and/or genetic mutation differences play a role in the etiology of CHDs by using single nucleotide polymorphism (SNP) genotyping arrays and whole exome sequencing of twin pairs discordant for CHDs. Our goal was to identify mutations present only in the affected twins, which could identify novel candidates for CHD susceptibility loci. We present a comprehensive analysis for the CNVs and genetic mutation results of the selected individuals but detected no consistent differences within the twin pairs. Our study confirms that chromosomal structure or genetic mutation differences do not seem to play a role in the MZ twins discordant for CHD.
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28
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Takahashi M, Hosomichi K, Yamaguchi T, Nagahama R, Yoshida H, Maki K, Marazita ML, Weinberg SM, Tajima A. Whole-genome sequencing in a pair of monozygotic twins with discordant cleft lip and palate subtypes. Oral Dis 2018; 24:1303-1309. [PMID: 29873870 DOI: 10.1111/odi.12910] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/15/2018] [Accepted: 05/31/2018] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Orofacial clefts (OFCs) are common and etiologically complex birth defects. This study explored potential genetic differences in a pair of Japanese monozygotic (MZ) twins with different forms of OFC using whole-genome sequencing. SUBJECTS AND METHODS One co-twin (MZ-1) presented with nonsyndromic bilateral cleft lip and palate; the other co-twin (MZ-2) had nonsyndromic bilateral cleft lip and unilateral left-sided cleft alveolus. Neither parent had an OFC. Craniofacial morphologic features and potential genetic differences were compared using standard cephalometry and whole-genome sequencing, respectively. RESULTS Morphologically, MZ-1 had a smaller vertical mandibular height, compared to MZ-2. However, no discordant genetic differences were detected. Moreover, both twins and their parents harbored rare candidate gene variants (GRHL3; TPM1) considered to be associated with OFCs. CONCLUSION The observed differences between MZ-1 and MZ-2 in craniofacial morphology assessed by cephalograms might be directly attributable to the effects of the OFC on growth and/or differences in surgical history, given the lack of any differences in genetic background. However, comparisons of discordant MZ twins should continue to identify novel candidates that might control OFC or that might partly explain the missing heritability for this common birth defect, in addition to understanding craniofacial growth and development.
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Affiliation(s)
- Masahiro Takahashi
- Department of Orthodontics, School of Dentistry, Showa University, Tokyo, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Tetsutaro Yamaguchi
- Department of Orthodontics, School of Dentistry, Showa University, Tokyo, Japan.,Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ryo Nagahama
- Department of Orthodontics, School of Dentistry, Showa University, Tokyo, Japan
| | - Hiroshi Yoshida
- Department of Orthodontics, School of Dentistry, Showa University, Tokyo, Japan
| | - Koutaro Maki
- Department of Orthodontics, School of Dentistry, Showa University, Tokyo, Japan
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania.,Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
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29
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Mohammadi A, Rashidi E, Amooeian VG. Brain, blood, cerebrospinal fluid, and serum biomarkers in schizophrenia. Psychiatry Res 2018; 265:25-38. [PMID: 29680514 DOI: 10.1016/j.psychres.2018.04.036] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/20/2018] [Accepted: 04/11/2018] [Indexed: 12/29/2022]
Abstract
Over the last decade, finding a reliable biomarker for the early detection of schizophrenia (Scz) has been a topic of interest. The main goal of the current review is to provide a comprehensive view of the brain, blood, cerebrospinal fluid (CSF), and serum biomarkers of Scz disease. Imaging studies have demonstrated that the volumes of the corpus callosum, thalamus, hippocampal formation, subiculum, parahippocampal gyrus, superior temporal gyrus, prefrontal and orbitofrontal cortices, and amygdala-hippocampal complex were reduced in patients diagnosed with Scz. It has been revealed that the levels of interleukin 1β (IL-1β), IL-6, IL-8, and TNF-α were increased in patients with Scz. Decreased mRNA levels of brain-derived neurotrophic factor (BDNF), tropomyosin receptor kinase B (TrkB), neurotrophin-3 (NT-3), nerve growth factor (NGF), and vascular endothelial growth factor (VEGF) genes have also been reported in Scz patients. Genes with known strong relationships with this disease include BDNF, catechol-O-methyltransferase (COMT), regulator of G-protein signaling 4 (RGS4), dystrobrevin-binding protein 1 (DTNBP1), neuregulin 1 (NRG1), Reelin (RELN), Selenium-binding protein 1 (SELENBP1), glutamic acid decarboxylase 67 (GAD 67), and disrupted in schizophrenia 1 (DISC1). The levels of dopamine, tyrosine hydroxylase (TH), serotonin or 5-hydroxytryptamine (5-HT) receptor 1A and B (5-HTR1A and 5-HTR1B), and 5-HT1B were significantly increased in Scz patients, while the levels of gamma-aminobutyric acid (GABA), 5-HT transporter (5-HTT), and 5-HT receptor 2A (5-HTR2A) were decreased. The increased levels of SELENBP1 and Glycogen synthase kinase 3 subunit α (GSK3α) genes in contrast with reduced levels of B-cell translocation gene 1 (BTG1), human leukocyte antigen DRB1 (HLA-DRB1), heterogeneous nuclear ribonucleoprotein A3 (HNRPA3), and serine/arginine-rich splicing factor 1 (SFRS1) genes have also been reported. This review covers various dysregulation of neurotransmitters and also highlights the strengths and weaknesses of studies attempting to identify candidate biomarkers.
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Affiliation(s)
- Alireza Mohammadi
- Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Ehsan Rashidi
- Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Ghasem Amooeian
- Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran
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30
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Richards R, Patel J, Stevenson K, Harbison S. Evaluation of massively parallel sequencing for forensic DNA methylation profiling. Electrophoresis 2018; 39:2798-2805. [DOI: 10.1002/elps.201800086] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/06/2018] [Accepted: 05/02/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Rebecca Richards
- Forensic Science Programme, School of Chemical Sciences; University of Auckland; Auckland New Zealand
- Institute of Environmental Science & Research Ltd. (ESR); Auckland New Zealand
| | - Jayshree Patel
- Institute of Environmental Science & Research Ltd. (ESR); Auckland New Zealand
| | - Kate Stevenson
- Institute of Environmental Science & Research Ltd. (ESR); Auckland New Zealand
| | - SallyAnn Harbison
- Institute of Environmental Science & Research Ltd. (ESR); Auckland New Zealand
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31
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Gould TD. Irving I. Gottesman (1930-2016): the multifactorial threshold model of complex phenotypes mediated by endophenotype strategies. GENES BRAIN AND BEHAVIOR 2018; 15:775-776. [PMID: 27681168 DOI: 10.1111/gbb.12345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 09/20/2016] [Indexed: 01/23/2023]
Affiliation(s)
- Todd D Gould
- Departments of Psychiatry, Pharmacology, and Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
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32
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Parveen R, Shamsi TN, Singh G, Athar T, Fatima S. Phytochemical analysis and In-vitro Biochemical Characterization of aqueous and methanolic extract of Triphala, a conventional herbal remedy. ACTA ACUST UNITED AC 2018; 17:126-136. [PMID: 29619331 PMCID: PMC5881245 DOI: 10.1016/j.btre.2018.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 01/15/2018] [Accepted: 02/05/2018] [Indexed: 11/26/2022]
Abstract
Triphala, an Indian ayurvedic triherbal formulation, is an equiproportional mixture of fruits of three herbs, amalaki (Emblica officinalis), haritaki (Terminalia chebula) and bibhitaki (Terminalia bellerica). The present study focused on phytocompounds detection and comparative analysis of various biochemical activities in the aqueous and methanolic extracts of triphala and its constituting herbs. Antioxidant activity was determined by 1, 1-diphenyl-2-picrylhydrazyl (DPPH), ferric reducing antioxidant power (FRAP), super oxide dismutase (SOD), catalase assay. Antibacterial potential was determined by broth dilution and agar well diffusion assays. Results revealed the presence of valuable bioactive compounds such as flavonoids, alkaloids, phenols, etc which might be responsible for biochemical activities. Extracts exhibited satisfactory radical-scavenging activity comparable with ascorbic acid. Methanolic extracts demonstrated higher antioxidant activity compared to aqueous extract. Extracts showed promising antibacterial potential against tested strain comparable to ampicillin. Hence, it can be concluded that triphala may be a promising candidate in pharmaceuticals and future medicine.
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Affiliation(s)
- Romana Parveen
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India
| | - Tooba Naz Shamsi
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India
| | - Gurjeet Singh
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201303, India
| | - Teeba Athar
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India
| | - Sadaf Fatima
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India
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33
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Laubach ZM, Perng W, Dolinoy DC, Faulk CD, Holekamp KE, Getty T. Epigenetics and the maintenance of developmental plasticity: extending the signalling theory framework. Biol Rev Camb Philos Soc 2018; 93:1323-1338. [PMID: 29356358 DOI: 10.1111/brv.12396] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 12/12/2022]
Abstract
Developmental plasticity, a phenomenon of importance in both evolutionary biology and human studies of the developmental origins of health and disease (DOHaD), enables organisms to respond to their environment based on previous experience without changes to the underlying nucleotide sequence. Although such phenotypic responses should theoretically improve an organism's fitness and performance in its future environment, this is not always the case. Herein, we first discuss epigenetics as an adaptive mechanism of developmental plasticity and use signaling theory to provide an evolutionary context for DOHaD phenomena within a generation. Next, we utilize signalling theory to identify determinants of adaptive developmental plasticity, detect sources of random variability - also known as process errors that affect maintenance of an epigenetic signal (DNA methylation) over time, and discuss implications of these errors for an organism's health and fitness. Finally, we apply life-course epidemiology conceptual models to inform study design and analytical strategies that are capable of parsing out the potential effects of process errors in the relationships among an organism's early environment, DNA methylation, and phenotype in a future environment. Ultimately, we hope to foster cross-talk and interdisciplinary collaboration between evolutionary biology and DOHaD epidemiology, which have historically remained separate despite a shared interest in developmental plasticity.
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Affiliation(s)
- Zachary M Laubach
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, U.S.A
| | - Wei Perng
- Department of Nutritional Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, U.S.A.,Department of Epidemiology, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, U.S.A
| | - Dana C Dolinoy
- Department of Nutritional Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, U.S.A.,Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, U.S.A
| | - Christopher D Faulk
- Department of Animal Sciences, University of Minnesota, 495B AnSc/VetMed, 1988 Fitch Avenue, St. Paul, MN, 55108, U.S.A
| | - Kay E Holekamp
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, U.S.A
| | - Thomas Getty
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, U.S.A
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Van Baak TE, Coarfa C, Dugué PA, Fiorito G, Laritsky E, Baker MS, Kessler NJ, Dong J, Duryea JD, Silver MJ, Saffari A, Prentice AM, Moore SE, Ghantous A, Routledge MN, Gong YY, Herceg Z, Vineis P, Severi G, Hopper JL, Southey MC, Giles GG, Milne RL, Waterland RA. Epigenetic supersimilarity of monozygotic twin pairs. Genome Biol 2018; 19:2. [PMID: 29310692 PMCID: PMC5759268 DOI: 10.1186/s13059-017-1374-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/06/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Monozygotic twins have long been studied to estimate heritability and explore epigenetic influences on phenotypic variation. The phenotypic and epigenetic similarities of monozygotic twins have been assumed to be largely due to their genetic identity. RESULTS Here, by analyzing data from a genome-scale study of DNA methylation in monozygotic and dizygotic twins, we identified genomic regions at which the epigenetic similarity of monozygotic twins is substantially greater than can be explained by their genetic identity. This "epigenetic supersimilarity" apparently results from locus-specific establishment of epigenotype prior to embryo cleavage during twinning. Epigenetically supersimilar loci exhibit systemic interindividual epigenetic variation and plasticity to periconceptional environment and are enriched in sub-telomeric regions. In case-control studies nested in a prospective cohort, blood DNA methylation at these loci years before diagnosis is associated with risk of developing several types of cancer. CONCLUSIONS These results establish a link between early embryonic epigenetic development and adult disease. More broadly, epigenetic supersimilarity is a previously unrecognized phenomenon that may contribute to the phenotypic similarity of monozygotic twins.
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Affiliation(s)
- Timothy E Van Baak
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Pierre-Antoine Dugué
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
| | - Giovanni Fiorito
- Department of Medical Sciences, University of Torino and Italian Institute for Genomic Medicine, Torino, Italy
| | - Eleonora Laritsky
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Maria S Baker
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Noah J Kessler
- MRC Unit The Gambia, Keneba, Gambia
- MRC International Nutrition Group at LSHTM, London, UK
| | - Jianrong Dong
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jack D Duryea
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Matt J Silver
- MRC Unit The Gambia, Keneba, Gambia
- MRC International Nutrition Group at LSHTM, London, UK
| | - Ayden Saffari
- MRC Unit The Gambia, Keneba, Gambia
- MRC International Nutrition Group at LSHTM, London, UK
| | - Andrew M Prentice
- MRC Unit The Gambia, Keneba, Gambia
- MRC International Nutrition Group at LSHTM, London, UK
| | - Sophie E Moore
- MRC Unit The Gambia, Keneba, Gambia
- Division of Women's Health, King's College London, London, UK
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | | | - Yun Yun Gong
- School of Food Science & Nutrition, University of Leeds, Leeds, UK
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Paolo Vineis
- MRC-PHE Center for Environment and Health, School of Public Health, Imperial College London, London, UK
- Italian Institute for Genomic Medicine, Torino, Italy
| | - Gianluca Severi
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
- Italian Institute for Genomic Medicine, Torino, Italy
- CESP Inserm, Facultés de medicine Université Paris-Sud, Paris, France
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
| | - Roger L Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
| | - Robert A Waterland
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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35
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Fadzan M, Bettany-Saltikov J. Etiological Theories of Adolescent Idiopathic Scoliosis: Past and Present. Open Orthop J 2017; 11:1466-1489. [PMID: 29399224 PMCID: PMC5759107 DOI: 10.2174/1874325001711011466] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/01/2017] [Accepted: 09/11/2017] [Indexed: 12/11/2022] Open
Abstract
Adolescent idiopathic scoliosis is one of the most common spinal deformities, yet its cause is unknown. Various theories look to biomechanical, neuromuscular, genetic, and environmental origins, yet our understanding of scoliosis etiology is still limited. Determining the cause of a disease is crucial to developing the most effective treatment. Associations made with scoliosis do not necessarily point to causality, and it is difficult to determine whether said associations are primary (playing a role in development) or secondary (develop as a result of scoliosis). Scoliosis is a complex condition with highly variable expression, even among family members, and likely has many causes. These causes could be similar among homogenous groups of AIS patients, or they could be individual. Here, we review the most prevalent theories of scoliosis etiology and recent trends in research.
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Affiliation(s)
- Maja Fadzan
- Scoliosis 3DC, 3 Baldwin Green Common, Suite 204, Woburn, MA 01801, USA
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Abstract
Human genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment. We envision future forensic applications of DNA methylation analysis that will broaden DNA-based forensic intelligence. Together with genetic prediction of appearance and biogeographic ancestry, epigenomic lifestyle prediction is expected to increase the ability of police to find unknown perpetrators of crime who are not identifiable using current forensic DNA profiling.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
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Laviola G, Zoratto F, Ingiosi D, Carito V, Huzard D, Fiore M, Macrì S. Low empathy-like behaviour in male mice associates with impaired sociability, emotional memory, physiological stress reactivity and variations in neurobiological regulations. PLoS One 2017; 12:e0188907. [PMID: 29200428 PMCID: PMC5714342 DOI: 10.1371/journal.pone.0188907] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 11/15/2017] [Indexed: 12/30/2022] Open
Abstract
Deficits in empathy have been proposed to constitute a hallmark of several psychiatric disturbances like conduct disorder, antisocial and narcissistic personality disorders. Limited sensitivity to punishment, shallow or deficient affect and reduced physiological reactivity to environmental stressors have been often reported to co-occur with limited empathy and contribute to the onset of antisocial phenotypes. Empathy in its simplest form (i.e. emotional contagion) is addressed in preclinical models through the evaluation of the social transmission of emotional states: mice exposed to a painful stimulus display a higher response if in the presence of a familiar individual experiencing a higher degree of discomfort, than in isolation. In the present study, we investigated whether a reduction of emotional contagion can be considered a predictor of reduced sociality, sensitivity to punishment and physiological stress reactivity. To this aim, we first evaluated emotional contagion in a group of Balb/cJ mice and then discretised their values in four quartiles. The upper (i.e. Emotional Contagion Prone, ECP) and the lower (i.e. Emotional Contagion Resistant, ECR) quartiles constituted the experimental groups. Our results indicate that mice in the lower quartile are characterized by reduced sociability, impaired memory of negative events and dampened hypothalamic-pituitary-adrenocortical reactivity to external stressors. Furthermore, in the absence of changes in oxytocin receptor density, we show that these mice exhibit elevated concentrations of oxytocin and vasopressin and reduced density of BDNF receptors in behaviourally-relevant brain areas. Thus, not only do present results translate to the preclinical investigation of psychiatric disturbances, but also they can contribute to the study of emotional contagion in terms of its adaptive significance.
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Affiliation(s)
- Giovanni Laviola
- Reference Centre for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità (ISS), Rome, Italy
- * E-mail:
| | - Francesca Zoratto
- Reference Centre for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Danilo Ingiosi
- Reference Centre for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Valentina Carito
- Institute of Cell Biology and Neurobiology, National Research Council of Italy (CNR), Rome, Italy
| | - Damien Huzard
- Laboratory of Behavioural Genetics, Brain Mind Institute, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marco Fiore
- Institute of Cell Biology and Neurobiology, National Research Council of Italy (CNR), Rome, Italy
| | - Simone Macrì
- Reference Centre for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità (ISS), Rome, Italy
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38
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Stern S, Kirst C, Bargmann CI. Neuromodulatory Control of Long-Term Behavioral Patterns and Individuality across Development. Cell 2017; 171:1649-1662.e10. [DOI: 10.1016/j.cell.2017.10.041] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 09/10/2017] [Accepted: 10/24/2017] [Indexed: 12/20/2022]
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39
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Maternal age generates phenotypic variation in Caenorhabditis elegans. Nature 2017; 552:106-109. [PMID: 29186117 PMCID: PMC5736127 DOI: 10.1038/nature25012] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 11/08/2017] [Indexed: 12/20/2022]
Abstract
Genetically identical individuals growing in the same environment often show substantial phenotypic variation within populations of organisms as diverse as bacteria1, nematodes2, rodents3 and humans4. With some exceptions5, the causes are poorly understood. We show here that isogenic Caenorhabditis elegans nematodes vary in their size at hatching, speed of development, growth rate, starvation resistance, fecundity, and also in the rate of development of their germline relative to that of somatic tissues. Surprisingly, we show that the primary cause of this variation is the age of an individual’s mother, with young mothers producing progeny impaired for many traits. We identify age-dependent changes in maternal provisioning of a lipoprotein complex (vitellogenin) to embryos as the molecular mechanism underlying variation in multiple traits throughout the life of an animal. The production of sub-optimal progeny by young mothers likely reflects a trade-off between the competing fitness traits of a short generation time and progeny survival and fecundity.
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Giegling I, Hosak L, Mössner R, Serretti A, Bellivier F, Claes S, Collier DA, Corrales A, DeLisi LE, Gallo C, Gill M, Kennedy JL, Leboyer M, Maier W, Marquez M, Massat I, Mors O, Muglia P, Nöthen MM, Ospina-Duque J, Owen MJ, Propping P, Shi Y, St Clair D, Thibaut F, Cichon S, Mendlewicz J, O'Donovan MC, Rujescu D. Genetics of schizophrenia: A consensus paper of the WFSBP Task Force on Genetics. World J Biol Psychiatry 2017; 18:492-505. [PMID: 28112043 DOI: 10.1080/15622975.2016.1268715] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Schizophrenia is a severe psychiatric disease affecting about 1% of the general population. The relative contribution of genetic factors has been estimated to be up to 80%. The mode of inheritance is complex, non-Mendelian, and in most cases involving the combined action of large numbers of genes. METHODS This review summarises recent efforts to identify genetic variants associated with schizophrenia detected, e.g., through genome-wide association studies, studies on copy-number variants or next-generation sequencing. RESULTS A large, new body of evidence on genetics of schizophrenia has accumulated over recent years. Many new robustly associated genetic loci have been detected. Furthermore, there is consensus that at least a dozen microdeletions and microduplications contribute to the disease. Genetic overlap between schizophrenia, other psychiatric disorders, and neurodevelopmental syndromes raised new questions regarding the current classification of psychiatric and neurodevelopmental diseases. CONCLUSIONS Future studies will address especially the functional characterisation of genetic variants. This will hopefully open the doors to our understanding of the pathophysiology of schizophrenia and other related diseases. Complementary, integrated systems biology approaches to genomics, transcriptomics, proteomics and metabolomics may also play crucial roles in enabling a precision medicine approach to the treatment of individual patients.
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Affiliation(s)
- Ina Giegling
- a Department of Psychiatry, Psychotherapy, and Psychosomatics , Martin Luther University of Halle-Wittenberg , Halle , Germany.,b Department of Psychiatry , Ludwig-Maximilians-University Munich , Munich , Germany
| | - Ladislav Hosak
- c Department of Psychiatriy , Charles University, Faculty of Medicine and University Hospital in Hradec Králové, Prague , Czech Republic
| | - Rainald Mössner
- d Department of Psychiatry and Psychotherapy , University of Tübingen , Tübingen , Germany
| | - Alessandro Serretti
- e Department of Biomedical and Neuromotor Sciences , University of Bologna , Bologna , Italy
| | - Frank Bellivier
- f Fondation Fondamental, Créteil, France AP-HP, GH Saint-Louis-Lariboisière-Fernand-Widal, Pôle Neurosciences , Paris , France.,g Equipe 1, Université Paris Diderot , Paris , France
| | - Stephan Claes
- h GRASP-Research Group, Department of Neuroscience , University of Leuven , Leuven , Belgium.,i Department of Neurosciences, University Psychiatric Center KU Leuven , Leuven , Belgium
| | - David A Collier
- j Social, Genetic and Developmental Psychiatry Centre , Institute of Psychiatry, King's College London , London , UK.,k Eli Lilly and Company Ltd, Erl Wood Manor , Surrey , UK
| | - Alejo Corrales
- l Argentinean Association of Biological Psychiatry , National University, UNT, Buenos Aires , Argentina
| | - Lynn E DeLisi
- m VA Boston Health Care System , Brockton , MA , USA.,n Department of Psychiatry , Harvard Medical School , Boston , MA , USA
| | - Carla Gallo
- o Departamento de Ciencias Celulares y Moleculares, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía , Universidad Peruana Cayetano Heredia , Lima , Peru
| | - Michael Gill
- p Neuropsychiatric Genetics Research Group, Department of Psychiatry , Trinity College Dublin , Dublin , Ireland
| | - James L Kennedy
- q Neurogenetics Section, Centre for Addiction and Mental Health , Toronto , ON , Canada.,r Centre for Addiction and Mental Health , Campbell Family Mental Health Research Institute , Toronto , ON , Canada.,s Department of Psychiatry , University of Toronto , Toronto , ON , Canada.,t Collaborative Program in Neuroscience, Institute of Medical Science, University of Toronto , Toronto , ON , Canada
| | - Marion Leboyer
- u Equipe Psychiatrie Translationnelle, Faculté de Médecine, Université Paris-Est Créteil, Inserm U955 , Créteil , France.,v DHU Pe-Psy, Pôle de Psychiatrie et d'Addictologie , AP-HP, Hôpitaux Universitaires Henri Mondor , Créteil , France.,w Pôle de Psychiatrie , Hôpital Albert Chenevier , Créteil , France.,x Fondation FondaMental , Créteil , France
| | - Wolfgang Maier
- y Department of Psychiatry and Psychotherapy , University of Bonn, Bonn , Germany
| | - Miguel Marquez
- z Asistencia, Docencia e Investigación en Neurociencia , Buenos Aires , Argentina
| | - Isabelle Massat
- aa UNI - ULB Neurosciences Institute, ULB , Bruxelles , Belgium.,ab National Fund of Scientific Research (FNRS) , Bruxelles , Belgium.,ac Laboratory of Experimental Neurology , ULB , Bruxelles , Belgium.,ad UR2NF - Neuropsychology and Functional Neuroimaging Research Unit, Centre de Recherche Cognition et Neurosciences , Université Libre de Bruxelles (ULB) , Bruxelles , Belgium
| | - Ole Mors
- ae Psychosis Research Unit , Aarhus University Hospital , Risskov , Denmark.,af The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus , Denmark
| | | | - Markus M Nöthen
- ah Head, Institute of Human Genetics, University of Bonn , Bonn , Germany.,ai Department of Genomics , Life and Brain Center , Bonn , Germany
| | - Jorge Ospina-Duque
- aj Grupo de Investigación en Psiquiatría, Departamento de Psiquiatría, Facultad de Medicina , Universidad de Antioquia , Medellín , Colombia
| | - Michael J Owen
- ak MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine , Cardiff University , Cardiff , UK.,al National Centre for Mental Health, Cardiff University , Cardiff , UK
| | | | - YongYong Shi
- an Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education , Shanghai Jiao Tong University , Shanghai , China.,ao Shandong Provincial Key Laboratory of Metabloic Disease, The Affiliated Hospital of Qingdao University , Qingdao , P.R. China.,ap Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University , Shanghai , P.R. China
| | - David St Clair
- aq Department of Psychiatry, University of Aberdeen, Institute of Medical Sciences , Aberdeen , UK
| | - Florence Thibaut
- ar INSERM U 894 Centre Psychiatry and Neurosciences , University Hospital Cochin (Site Tarnier), University Sorbonne Paris Cité (Faculty of Medicine Paris Descartes) , Paris , France
| | - Sven Cichon
- ah Head, Institute of Human Genetics, University of Bonn , Bonn , Germany.,ai Department of Genomics , Life and Brain Center , Bonn , Germany.,as Division of Medical Genetics, Department of Biomedicine , University of Basel , Basel , Switzerland.,at Genomic Imaging, Institute of Neuroscience and Medicine , Research Center Juelich , Juelich , Germany
| | - Julien Mendlewicz
- au Laboratoire de Psychologie Medicale, Centre Europe´en de Psychologie Medicale , Universite´ Libre de Bruxelles and Psy Pluriel , Brussels , Belgium
| | - Michael C O'Donovan
- ak MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine , Cardiff University , Cardiff , UK.,al National Centre for Mental Health, Cardiff University , Cardiff , UK
| | - Dan Rujescu
- a Department of Psychiatry, Psychotherapy, and Psychosomatics , Martin Luther University of Halle-Wittenberg , Halle , Germany.,b Department of Psychiatry , Ludwig-Maximilians-University Munich , Munich , Germany
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41
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Dulka BN, Bourdon AK, Clinard CT, Muvvala MBK, Campagna SR, Cooper MA. Metabolomics reveals distinct neurochemical profiles associated with stress resilience. Neurobiol Stress 2017; 7:103-112. [PMID: 28828396 PMCID: PMC5552108 DOI: 10.1016/j.ynstr.2017.08.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/11/2017] [Accepted: 08/05/2017] [Indexed: 11/27/2022] Open
Abstract
Acute social defeat represents a naturalistic form of conditioned fear and is an excellent model in which to investigate the biological basis of stress resilience. While there is growing interest in identifying biomarkers of stress resilience, until recently, it has not been feasible to associate levels of large numbers of neurochemicals and metabolites to stress-related phenotypes. The objective of the present study was to use an untargeted metabolomics approach to identify known and unknown neurochemicals in select brain regions that distinguish susceptible and resistant individuals in two rodent models of acute social defeat. In the first experiment, male mice were first phenotyped as resistant or susceptible. Then, mice were subjected to acute social defeat, and tissues were immediately collected from the ventromedial prefrontal cortex (vmPFC), basolateral/central amygdala (BLA/CeA), nucleus accumbens (NAc), and dorsal hippocampus (dHPC). Ultra-high performance liquid chromatography coupled with high resolution mass spectrometry (UPLC-HRMS) was used for the detection of water-soluble neurochemicals. In the second experiment, male Syrian hamsters were paired in daily agonistic encounters for 2 weeks, during which they formed stable dominant-subordinate relationships. Then, 24 h after the last dominance encounter, animals were exposed to acute social defeat stress. Immediately after social defeat, tissue was collected from the vmPFC, BLA/CeA, NAc, and dHPC for analysis using UPLC-HRMS. Although no single biomarker characterized stress-related phenotypes in both species, commonalities were found. For instance, in both model systems, animals resistant to social defeat stress also show increased concentration of molecules to protect against oxidative stress in the NAc and vmPFC. Additionally, in both mice and hamsters, unidentified spectral features were preliminarily annotated as potential targets for future experiments. Overall, these findings suggest that a metabolomics approach can identify functional groups of neurochemicals that may serve as novel targets for the diagnosis, treatment, or prevention of stress-related mental illness.
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Affiliation(s)
- Brooke N Dulka
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, United States
| | - Allen K Bourdon
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, United States
| | - Catherine T Clinard
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, United States
| | - Mohan B K Muvvala
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, United States
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, United States.,Biological Small Molecule Mass Spectrometry Core, University of Tennessee, Knoxville, TN 37996, United States
| | - Matthew A Cooper
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, United States
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42
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Holtkötter H, Beyer V, Schwender K, Glaub A, Johann KS, Schürenkamp M, Sibbing U, Banken S, Wiegand P, Pfeiffer H, Dennany L, Vennemann M, Vennemann M. Independent validation of body fluid-specific CpG markers and construction of a robust multiplex assay. Forensic Sci Int Genet 2017; 29:261-268. [DOI: 10.1016/j.fsigen.2017.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/18/2017] [Accepted: 05/06/2017] [Indexed: 11/25/2022]
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43
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Bierbach D, Laskowski KL, Wolf M. Behavioural individuality in clonal fish arises despite near-identical rearing conditions. Nat Commun 2017; 8:15361. [PMID: 28513582 PMCID: PMC5442312 DOI: 10.1038/ncomms15361] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 03/23/2017] [Indexed: 02/07/2023] Open
Abstract
Behavioural individuality is thought to be caused by differences in genes and/or environmental conditions. Therefore, if these sources of variation are removed, individuals are predicted to develop similar phenotypes lacking repeatable individual variation. Moreover, even among genetically identical individuals, direct social interactions are predicted to be a powerful factor shaping the development of individuality. We use tightly controlled ontogenetic experiments with clonal fish, the Amazon molly (Poecilia formosa), to test whether near-identical rearing conditions and lack of social contact dampen individuality. In sharp contrast to our predictions, we find that (i) substantial individual variation in behaviour emerges among genetically identical individuals isolated directly after birth into highly standardized environments and (ii) increasing levels of social experience during ontogeny do not affect levels of individual behavioural variation. In contrast to the current research paradigm, which focuses on genes and/or environmental drivers, our findings suggest that individuality might be an inevitable and potentially unpredictable outcome of development. Genetically-identical animals experiencing the same environmental conditions should develop, in theory, identical behavioral traits. However, Bierbach et al. show here that behavioral differences still emerge among cloned fish under tightly controlled experimental conditions.
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Affiliation(s)
- David Bierbach
- Department of Biology and Ecology of Fishes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587 Berlin, Germany
| | - Kate L Laskowski
- Department of Biology and Ecology of Fishes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587 Berlin, Germany
| | - Max Wolf
- Department of Biology and Ecology of Fishes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587 Berlin, Germany
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44
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Variation in gene expression within clones of the earthworm Dendrobaena octaedra. PLoS One 2017; 12:e0174960. [PMID: 28384196 PMCID: PMC5383104 DOI: 10.1371/journal.pone.0174960] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 03/19/2017] [Indexed: 12/23/2022] Open
Abstract
Gene expression is highly plastic, which can help organisms to both acclimate and adapt to changing environments. Possible variation in gene expression among individuals with the same genotype (among clones) is not widely considered, even though it could impact the results of studies that focus on gene expression phenotypes, for example studies using clonal lines. We examined the extent of within and between clone variation in gene expression in the earthworm Dendrobaena octaedra, which reproduces through apomictic parthenogenesis. Five microsatellite markers were developed and used to confirm that offspring are genetic clones of their parent. After that, expression of 12 genes was measured from five individuals each from six clonal lines after exposure to copper contaminated soil. Variation in gene expression was higher over all genotypes than within genotypes, as initially assumed. A subset of the genes was also examined in the offspring of exposed individuals in two of the clonal lines. In this case, variation in gene expression within genotypes was as high as that observed over all genotypes. One gene in particular (chymotrypsin inhibitor) also showed significant differences in the expression levels among genetically identical individuals. Gene expression can vary considerably, and the extent of variation may depend on the genotypes and genes studied. Ensuring a large sample, with many different genotypes, is critical in studies comparing gene expression phenotypes. Researchers should be especially cautious inferring gene expression phenotypes when using only a single clonal or inbred line, since the results might be specific to only certain genotypes.
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45
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Clark WS, Galen SC, Hull JM, Mayo MA, Witt CC. Contrasting molecular and morphological evidence for the identification of an anomalous Buteo: a cautionary tale for hybrid diagnosis. PeerJ 2017; 5:e2850. [PMID: 28097061 PMCID: PMC5228515 DOI: 10.7717/peerj.2850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 12/01/2016] [Indexed: 11/29/2022] Open
Abstract
An adult Buteo was found dead as a road-kill south of Sacramento, California, and was thought to represent the first state record of the eastern Red-shouldered Hawk (B. lineatus lineatus;). It is now a specimen in the Museum of Wildlife and Fisheries Biology (WFB 4816) at the University of California, Davis. We examined this specimen and found that many of its plumage characters differed from all other adult Red-shouldered Hawks examined, including nominate adults. Plumage markings and measurements were intermediate between Red-tailed Hawk (Buteo jamaicensis, ssp calurus) and Red-shouldered Hawk (ssp elegans), leading us to hypothesize that the bird was a hybrid. However, mtDNA sequences and nuDNA microsatellites proved definitively that the bird was a Red-shouldered Hawk, most likely of eastern origin. This case illustrates that apparent hybrids or apparent vagrants could be individuals with anomalous phenotypes caused by rare genetic variation or novel epigenetic effects.
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Affiliation(s)
| | - Spencer C Galen
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, United States
| | - Joshua M Hull
- Department of Animal Science, University of California, Davis, CA, United States
| | - Megan A Mayo
- Department of Animal Science, University of California, Davis, CA, United States
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, United States
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46
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Dong N, Feng ZP. Inverse Relationship between Basal Pacemaker Neuron Activity and Aversive Long-Term Memory Formation in Lymnaea stagnalis. Front Cell Neurosci 2017; 10:297. [PMID: 28101006 PMCID: PMC5209385 DOI: 10.3389/fncel.2016.00297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 12/15/2016] [Indexed: 11/18/2022] Open
Abstract
Learning and memory formation are essential physiological functions. While quiescent neurons have long been the focus of investigations into the mechanisms of memory formation, there is increasing evidence that spontaneously active neurons also play key roles in this process and possess distinct rules of activity-dependent plasticity. In this study, we used a well-defined aversive learning model of aerial respiration in the mollusk Lymnaea stagnalis (L. stagnalis) to study the role of basal firing activity of the respiratory pacemaker neuron Right Pedal Dorsal 1 (RPeD1) as a determinant of aversive long-term memory (LTM) formation. We investigated the relationship between basal aerial respiration behavior and RPeD1 firing activity, and examined aversive LTM formation and neuronal plasticity in animals exhibiting different basal aerial respiration behavior. We report that animals with higher basal aerial respiration behavior exhibited early responses to operant conditioning and better aversive LTM formation. Early behavioral response to the conditioning procedure was associated with biphasic enhancements in the membrane potential, spontaneous firing activity and gain of firing response, with an early phase spanning the first 2 h after conditioning and a late phase that is observed at 24 h. Taken together, we provide the first evidence suggesting that lower neuronal activity at the time of learning may be correlated with better memory formation in spontaneously active neurons. Our findings provide new insights into the diversity of cellular rules of plasticity underlying memory formation.
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Affiliation(s)
- Nancy Dong
- Department of Physiology, University of Toronto Toronto, ON, Canada
| | - Zhong-Ping Feng
- Department of Physiology, University of Toronto Toronto, ON, Canada
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47
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Hirota T, Tanaka T, Takesue H, Ieiri I. Epigenetic regulation of drug transporter expression in human tissues. Expert Opin Drug Metab Toxicol 2016; 13:19-30. [DOI: 10.1080/17425255.2017.1230199] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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48
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Joonè CJ, De Cramer KGM, Nöthling JO. The first case of genetically confirmed monozygotic twinning in the dog. Reprod Domest Anim 2016; 51:835-9. [DOI: 10.1111/rda.12746] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/03/2016] [Indexed: 01/12/2023]
Affiliation(s)
- CJ Joonè
- Department of Production Animal Studies; Faculty of Veterinary Science; University of Pretoria; Pretoria South Africa
- Division of Tropical Health and Medicine; College of Public Health; Medical and Veterinary Sciences; James Cook University; Townsville Australia
| | - KGM De Cramer
- Rant en Dal Animal Hospital; Mogale City South Africa
| | - JO Nöthling
- Department of Production Animal Studies; Faculty of Veterinary Science; University of Pretoria; Pretoria South Africa
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49
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Triantaphyllopoulos KA, Ikonomopoulos I, Bannister AJ. Epigenetics and inheritance of phenotype variation in livestock. Epigenetics Chromatin 2016. [PMID: 27446239 DOI: 10.1186/s13072‐016‐0081‐5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Epigenetic inheritance plays a crucial role in many biological processes, such as gene expression in early embryo development, imprinting and the silencing of transposons. It has recently been established that epigenetic effects can be inherited from one generation to the next. Here, we review examples of epigenetic mechanisms governing animal phenotype and behaviour, and we discuss the importance of these findings in respect to animal studies, and livestock in general. Epigenetic parameters orchestrating transgenerational effects, as well as heritable disorders, and the often-overlooked areas of livestock immunity and stress, are also discussed. We highlight the importance of nutrition and how it is linked to epigenetic alteration. Finally, we describe how our understanding of epigenetics is underpinning the latest cancer research and how this can be translated into directed efforts to improve animal health and welfare.
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Affiliation(s)
- Kostas A Triantaphyllopoulos
- Department of Animal Breeding and Husbandry, Faculty of Animal Science and Aquaculture, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
| | - Ioannis Ikonomopoulos
- Department of Anatomy and Physiology of Farm Animals, Faculty of Animal Science and Aquaculture, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
| | - Andrew J Bannister
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
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50
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Triantaphyllopoulos KA, Ikonomopoulos I, Bannister AJ. Epigenetics and inheritance of phenotype variation in livestock. Epigenetics Chromatin 2016; 9:31. [PMID: 27446239 PMCID: PMC4955263 DOI: 10.1186/s13072-016-0081-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 07/06/2016] [Indexed: 01/04/2023] Open
Abstract
Epigenetic inheritance plays a crucial role in many biological processes, such as gene expression in early embryo development, imprinting and the silencing of transposons. It has recently been established that epigenetic effects can be inherited from one generation to the next. Here, we review examples of epigenetic mechanisms governing animal phenotype and behaviour, and we discuss the importance of these findings in respect to animal studies, and livestock in general. Epigenetic parameters orchestrating transgenerational effects, as well as heritable disorders, and the often-overlooked areas of livestock immunity and stress, are also discussed. We highlight the importance of nutrition and how it is linked to epigenetic alteration. Finally, we describe how our understanding of epigenetics is underpinning the latest cancer research and how this can be translated into directed efforts to improve animal health and welfare.
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Affiliation(s)
- Kostas A. Triantaphyllopoulos
- />Department of Animal Breeding and Husbandry, Faculty of Animal Science and Aquaculture, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
| | - Ioannis Ikonomopoulos
- />Department of Anatomy and Physiology of Farm Animals, Faculty of Animal Science and Aquaculture, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
| | - Andrew J. Bannister
- />Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
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