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Vacquier VD, Hamdoun A. Cold storage and cryopreservation methods for spermatozoa of the sea urchins Lytechinus pictus and Strongylocentrotus purpuratus. Dev Dyn 2024. [PMID: 38340021 DOI: 10.1002/dvdy.691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Sea urchins have contributed greatly to knowledge of fertilization, embryogenesis, and cell biology. However, until now, they have not been genetic model organisms because of their long generation times and lack of tools for husbandry and gene manipulation. We recently established the sea urchin Lytechinus pictus, as a multigenerational model Echinoderm, because of its relatively short generation time of 4-6 months and ease of laboratory culture. To take full advantage of this new multigenerational species, methods are needed to biobank and share genetically modified L. pictus sperm. RESULTS Here, we describe a method, based on sperm ion physiology that maintains L. pictus and Strongylocentrotus purpuratus sperm fertilizable for at least 5-10 weeks when stored at 0°C. We also describe a new method to cryopreserve sperm of both species. Sperm of both species can be frozen and thawed at least twice and still give rise to larvae that undergo metamorphosis. CONCLUSIONS The simple methods we describe work well for both species, achieving >90% embryo development and producing larvae that undergo metamorphosis to juvenile adults. We hope that these methods will be useful to others working on marine invertebrate sperm.
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Affiliation(s)
- Victor D Vacquier
- Center for Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Amro Hamdoun
- Center for Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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Alipanah M, Roudbari Z, Momen M, Esmailizadeh A. Impact of inclusion non-additive effects on genome-wide association and variance's components in Scottish black sheep. Anim Biotechnol 2023; 34:3765-3773. [PMID: 37343283 DOI: 10.1080/10495398.2023.2224845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
CONTEXT It's well-documented that most economic traits have a complex genetic structure that is controlled by additive and non-additive gene actions. Hence, knowledge of the underlying genetic architecture of such complex traits could aid in understanding how these traits respond to the selection in breeding and mating programs. Computing and having estimates of the non-additive effect for economic traits in sheep using genome-wide information can be important because; non-additive genes play an important role in the prediction accuracy of genomic breeding values and the genetic response to the selection. AIM This study aimed to assess the impact of non-additive effects (dominance and epistasis) on the estimation of genetic parameters for body weight traits in sheep. METHODS This study used phenotypic and genotypic belonging to 752 Scottish Blackface lambs. Three live weight traits considered in this study were included in body weight at 16, 20, and 24 weeks). Three genetic models including additive (AM), additive + dominance (ADM), and additive + dominance + epistasis (ADEM), were used. KEY RESULTS The narrow sense heritability for weight at 16 weeks of age (BW16) were 0.39, 0.35, and 0.23, for 20 weeks of age (BW20) were 0.55, 0.54, and 0.42, and finally for 24 weeks of age (BW24) were 0.16, 0.12, and 0.02, using the AM, ADM, and ADEM models, respectively. The additive genetic model significantly outperformed the non-additive genetic model (p < 0.01). The dominance variance of the BW16, BW20, and BW24 accounted for 38, 6, and 30% of the total phenotypic, respectively. Moreover, the epistatic variance accounted for 39, 0.39, and 47% of the total phenotypic variances of these traits, respectively. In addition, our results indicated that the most important SNPs for live weight traits are on chromosomes 3 (three SNPS including s12606.1, OAR3_221188082.1, and OAR3_4106875.1), 8 (OAR8_16468019.1, OAR8_18067475.1, and OAR8_18043643.1), and 19 (OAR19_18010247.1), according to the genome-wide association analysis using additive and non-additive genetic model. CONCLUSIONS The results emphasized that the non-additive genetic effects play an important role in controlling body weight variation at the age of 16-24 weeks in Scottish Blackface lambs. IMPLICATIONS It is expected that using a high-density SNP panel and the joint modeling of both additive and non-additive effects can lead to better estimation and prediction of genetic parameters.
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Affiliation(s)
- Masoud Alipanah
- Department of Plant Production, University of Torbat Heydarieh, Torbat-e Heydarieh, Iran
| | - Zahra Roudbari
- Department of Animal Science, University of Jiroft, Jiroft, Iran
| | - Mehdi Momen
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Ali Esmailizadeh
- Department of Animal Science, Shahid Bahonar University of Kerman, Kerman, Iran
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Encina A, Ligero M, Sánchez-Guerrero MJ, Rodríguez-Sainz de los Terreros A, Bartolomé E, Valera M. Phenotypic and Genetic Study of the Presence of Hair Whorls in Pura Raza Español Horses. Animals (Basel) 2023; 13:2943. [PMID: 37760344 PMCID: PMC10525084 DOI: 10.3390/ani13182943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Hair whorls are a hereditary feature in horses that may be associated with temperament and coat color. Hair whorls are described as changes in the hair pattern and may take various forms, such as circular and linear whorls. We first carried out a frequency analysis of hair whorls (circular and linear). Next, a Generalized Non-Linear Model was computed to assess the significance of some potential influencing factors, and a genetic parameter estimation was performed. ENDOG software v4.8 was used to estimate the inbreeding coefficient of all the animals analyzed. It was more common to find horses with circular hair whorls than with linear whorls. The heritability ranges obtained were, in general, medium-high for both circular whorls (0.20 to 0.90) and linear whorls (0.44 to 0.84). High positive correlations were found on the between left and right positions, indicating a tendency to symmetry in certain locations. The laterality of hair whorls was also evidenced, with the biggest concentration on the left-hand side, particularly in gray horses, showing circular whorls below the central line of eyes, which has been associated in a previous paper with a calmer and more docile temperament.
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Affiliation(s)
- Ana Encina
- Real Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), 41014 Sevilla, Spain;
| | - Manuel Ligero
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniaría Agronómica, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.L.); (M.J.S.-G.); (E.B.); (M.V.)
| | - María José Sánchez-Guerrero
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniaría Agronómica, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.L.); (M.J.S.-G.); (E.B.); (M.V.)
| | | | - Ester Bartolomé
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniaría Agronómica, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.L.); (M.J.S.-G.); (E.B.); (M.V.)
| | - Mercedes Valera
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniaría Agronómica, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.L.); (M.J.S.-G.); (E.B.); (M.V.)
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Miguel Sanz C, Martinez Navarro M, Caballero Diaz D, Sanchez-Elexpuru G, Di Donato V. Toward the use of novel alternative methods in epilepsy modeling and drug discovery. Front Neurol 2023; 14:1213969. [PMID: 37719765 PMCID: PMC10501616 DOI: 10.3389/fneur.2023.1213969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/14/2023] [Indexed: 09/19/2023] Open
Abstract
Epilepsy is a chronic brain disease and, considering the amount of people affected of all ages worldwide, one of the most common neurological disorders. Over 20 novel antiseizure medications (ASMs) have been released since 1993, yet despite substantial advancements in our understanding of the molecular mechanisms behind epileptogenesis, over one-third of patients continue to be resistant to available therapies. This is partially explained by the fact that the majority of existing medicines only address seizure suppression rather than underlying processes. Understanding the origin of this neurological illness requires conducting human neurological and genetic studies. However, the limitation of sample sizes, ethical concerns, and the requirement for appropriate controls (many patients have already had anti-epileptic medication exposure) in human clinical trials underscore the requirement for supplemental models. So far, mammalian models of epilepsy have helped to shed light on the underlying causes of the condition, but the high costs related to breeding of the animals, low throughput, and regulatory restrictions on their research limit their usefulness in drug screening. Here, we present an overview of the state of art in epilepsy modeling describing gold standard animal models used up to date and review the possible alternatives for this research field. Our focus will be mainly on ex vivo, in vitro, and in vivo larval zebrafish models contributing to the 3R in epilepsy modeling and drug screening. We provide a description of pharmacological and genetic methods currently available but also on the possibilities offered by the continued development in gene editing methodologies, especially CRISPR/Cas9-based, for high-throughput disease modeling and anti-epileptic drugs testing.
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Córdoba SC, Tong H, Burgos A, Zhu F, Alseekh S, Fernie AR, Nikoloski Z. Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism. Nat Commun 2023; 14:4897. [PMID: 37580345 PMCID: PMC10425450 DOI: 10.1038/s41467-023-40644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/04/2023] [Indexed: 08/16/2023] Open
Abstract
Lipids play fundamental roles in regulating agronomically important traits. Advances in plant lipid metabolism have until recently largely been based on reductionist approaches, although modulation of its components can have system-wide effects. However, existing models of plant lipid metabolism provide lumped representations, hindering detailed study of component modulation. Here, we present the Plant Lipid Module (PLM) which provides a mechanistic description of lipid metabolism in the Arabidopsis thaliana rosette. We demonstrate that the PLM can be readily integrated in models of A. thaliana Col-0 metabolism, yielding accurate predictions (83%) of single lethal knock-outs and 75% concordance between measured transcript and predicted flux changes under extended darkness. Genome-wide associations with fluxes obtained by integrating the PLM in diel condition- and accession-specific models identify up to 65 candidate genes modulating A. thaliana lipid metabolism. Using mutant lines, we validate up to 40% of the candidates, paving the way for identification of metabolic gene function based on models capturing natural variability in metabolism.
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Affiliation(s)
- Sandra Correa Córdoba
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
| | - Hao Tong
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Asdrúbal Burgos
- Department of Zoology and Botany, University of Guadalajara, Guadalajara, Mexico
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Hubei Hongshan Laboratory, National Key Laboratory for Germplasm Innovation and Utilization for Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Saleh Alseekh
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Alisdair R Fernie
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria.
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Zengel J, Wang YX, Seo JW, Ning K, Hamilton JN, Wu B, Raie M, Holbrook C, Su S, Clements DR, Pillay S, Puschnik AS, Winslow MM, Idoyaga J, Nagamine CM, Sun Y, Mahajan VB, Ferrara KW, Blau HM, Carette JE. Hardwiring tissue-specific AAV transduction in mice through engineered receptor expression. Nat Methods 2023; 20:1070-1081. [PMID: 37291262 PMCID: PMC10333121 DOI: 10.1038/s41592-023-01896-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 04/25/2023] [Indexed: 06/10/2023]
Abstract
The development of transgenic mouse models that express genes of interest in specific cell types has transformed our understanding of basic biology and disease. However, generating these models is time- and resource-intensive. Here we describe a model system, SELective Expression and Controlled Transduction In Vivo (SELECTIV), that enables efficient and specific expression of transgenes by coupling adeno-associated virus (AAV) vectors with Cre-inducible overexpression of the multi-serotype AAV receptor, AAVR. We demonstrate that transgenic AAVR overexpression greatly increases the efficiency of transduction of many diverse cell types, including muscle stem cells, which are normally refractory to AAV transduction. Superior specificity is achieved by combining Cre-mediated AAVR overexpression with whole-body knockout of endogenous Aavr, which is demonstrated in heart cardiomyocytes, liver hepatocytes and cholinergic neurons. The enhanced efficacy and exquisite specificity of SELECTIV has broad utility in development of new mouse model systems and expands the use of AAV for gene delivery in vivo.
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Affiliation(s)
- James Zengel
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yu Xin Wang
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Genetic Disorders and Aging, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jai Woong Seo
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ke Ning
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | - James N Hamilton
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bo Wu
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marina Raie
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Colin Holbrook
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shiqi Su
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Derek R Clements
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Sirika Pillay
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Andreas S Puschnik
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Juliana Idoyaga
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Claude M Nagamine
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Yang Sun
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
- Palo Alto Veterans Administration, Palo Alto, CA, USA
| | - Vinit B Mahajan
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
- Palo Alto Veterans Administration, Palo Alto, CA, USA
| | - Katherine W Ferrara
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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Brown PJB, Chang JH, Fuqua C. Agrobacterium tumefaciens: a Transformative Agent for Fundamental Insights into Host-Microbe Interactions, Genome Biology, Chemical Signaling, and Cell Biology. J Bacteriol 2023; 205:e0000523. [PMID: 36892285 PMCID: PMC10127608 DOI: 10.1128/jb.00005-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Agrobacterium tumefaciens incites the formation of readily visible macroscopic structures known as crown galls on plant tissues that it infects. Records from biologists as early as the 17th century noted these unusual plant growths and began examining the basis for their formation. These studies eventually led to isolation of the infectious agent, A. tumefaciens, and decades of study revealed the remarkable mechanisms by which A. tumefaciens causes crown gall through stable horizontal genetic transfer to plants. This fundamental discovery generated a barrage of applications in the genetic manipulation of plants that is still under way. As a consequence of the intense study of A. tumefaciens and its role in plant disease, this pathogen was developed as a model for the study of critical processes that are shared by many bacteria, including host perception during pathogenesis, DNA transfer and toxin secretion, bacterial cell-cell communication, plasmid biology, and more recently, asymmetric cell biology and composite genome coordination and evolution. As such, studies of A. tumefaciens have had an outsized impact on diverse areas within microbiology and plant biology that extend far beyond its remarkable agricultural applications. In this review, we attempt to highlight the colorful history of A. tumefaciens as a study system, as well as current areas that are actively demonstrating its value and utility as a model microorganism.
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Affiliation(s)
- Pamela J. B. Brown
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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Gebru NT, Hill SE, Blair LJ. Genetically engineered mouse models of FK506-binding protein 5. J Cell Biochem 2023:10.1002/jcb.30374. [PMID: 36780339 PMCID: PMC10423308 DOI: 10.1002/jcb.30374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/25/2022] [Accepted: 01/15/2023] [Indexed: 02/14/2023]
Abstract
FK506 binding protein 51 (FKBP51) is a molecular chaperone that influences stress response. In addition to having an integral role in the regulation of steroid hormone receptors, including glucocorticoid receptor, FKBP51 has been linked with several biological processes including metabolism and neuronal health. Genetic and epigenetic alterations in the gene that encodes FKBP51, FKBP5, are associated with increased susceptibility to multiple neuropsychiatric disorders, which has fueled much of the research on this protein. Because of the complexity of these processes, animal models have been important in understanding the role of FKBP51. This review examines each of the current mouse models of FKBP5, which include whole animal knockout, conditional knockout, overexpression, and humanized mouse models. The generation of each model and observational details are discussed, including behavioral phenotypes, molecular changes, and electrophysiological alterations basally and following various challenges. While much has been learned through these models, there are still many aspects of FKBP51 biology that remain opaque and future studies are needed to help illuminate these current gaps in knowledge. Overall, FKBP5 continues to be an exciting potential target for stress-related disorders.
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Affiliation(s)
- Niat T. Gebru
- USF Health Byrd Alzheimer’s Institute, University of South Florida, 4001 E. Fletcher Ave. Tampa, Florida 33613, United States
- Department of Molecular Medicine, University of South Florida, 4001 E. Fletcher Ave. Tampa, Florida 33613, United States
| | - Shannon E. Hill
- USF Health Byrd Alzheimer’s Institute, University of South Florida, 4001 E. Fletcher Ave. Tampa, Florida 33613, United States
- Department of Molecular Medicine, University of South Florida, 4001 E. Fletcher Ave. Tampa, Florida 33613, United States
| | - Laura J. Blair
- USF Health Byrd Alzheimer’s Institute, University of South Florida, 4001 E. Fletcher Ave. Tampa, Florida 33613, United States
- Department of Molecular Medicine, University of South Florida, 4001 E. Fletcher Ave. Tampa, Florida 33613, United States
- Research Service, James A. Haley Veterans Hospital, 13000 Bruce B Downs Blvd, Tampa, FL 33612, United States
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Madhariya R, Dixena B, Ram A, Vyas A, Jain AK. Experimental Animal Models: Tools to Investigate Antidiabetic Activity. Curr Pharm Des 2023; 29:79-94. [PMID: 36545714 DOI: 10.2174/1381612829666221220115649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 10/17/2022] [Accepted: 10/27/2022] [Indexed: 12/24/2022]
Abstract
About 2.8% of the global population are being suffered from Diabetes mellitus. Diabetes mellitus is a group of metabolic disorders that is characterized by an absolute lack of insulin and resulting in hyperglycemia. To overcome the challenges, many antidiabetic drugs are being used, and research is being carried out in search of more effective anti-diabetic drugs. To study the effectiveness of antidiabetic drugs, many diabetic models, chemicals, and diabetogenic hormones were used at the research level. In this review, we summarised various animal models used, chemicals that induce diabetes, their properties, and the mechanism of action of these models. Further, diabetes mellitus is generally induced in laboratory animals by several methods that include: chemical, surgical and genetic manipulations. To better understand both the pathogenesis and potential therapeutic agents, appropriate animal models of type 1 & type 2 diabetes mellitus are needed. However, for an animal model to have relevance to the study of diabetes, either the characteristics of the animal model should mirror the pathophysiology and natural history of diabetes or the model should develop complications of diabetes with an etiology similar to that of the human condition. There appears to be no single animal model that encompasses all of these characteristics, but there are many that provide very similar characteristics in one or more aspects of diabetes in humans. The use of the appropriate animal model based on these similarities can provide much-needed data on pathophysiological mechanisms operative in human diabetes.
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Affiliation(s)
- Rashmi Madhariya
- Department of Pharmacy, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur (C.G.), 495009, India
| | - Bhupendra Dixena
- Department of Pharmacy, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur (C.G.), 495009, India
| | - Alpana Ram
- Department of Pharmacy, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur (C.G.), 495009, India
| | - Amber Vyas
- Department of Pt. Ravishankar Shukla University, Pandit Ravishankar Shukla University, Raipur (C.G.), 492010, India
| | - Akhlesh Kumar Jain
- Department of Pharmacy, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur (C.G.), 495009, India
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Habimana V, Ekine-Dzivenu CC, Nguluma AS, Nziku ZC, Morota G, Chenyambuga SW, Mrode R. Genes and models for estimating genetic parameters for heat tolerance in dairy cattle. Front Genet 2023; 14:1127175. [PMID: 36923799 PMCID: PMC10009153 DOI: 10.3389/fgene.2023.1127175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/14/2023] [Indexed: 03/02/2023] Open
Abstract
Dairy cattle are highly susceptible to heat stress. Heat stress causes a decline in milk yield, reduced dry matter intake, reduced fertility rates, and alteration of physiological traits (e.g., respiration rate, rectal temperature, heart rates, pulse rates, panting score, sweating rates, and drooling score) and other biomarkers (oxidative heat stress biomarkers and stress response genes). Considering the significant effect of global warming on dairy cattle farming, coupled with the aim to reduce income losses of dairy cattle farmers and improve production under hot environment, there is a need to develop heat tolerant dairy cattle that can grow, reproduce and produce milk reasonably under the changing global climate and increasing temperature. The identification of heat tolerant dairy cattle is an alternative strategy for breeding thermotolerant dairy cattle for changing climatic conditions. This review synthesizes information pertaining to quantitative genetic models that have been applied to estimate genetic parameters for heat tolerance and relationship between measures of heat tolerance and production and reproductive performance traits in dairy cattle. Moreover, the review identified the genes that have been shown to influence heat tolerance in dairy cattle and evaluated the possibility of using them in genomic selection programmes. Combining genomics information with environmental, physiological, and production parameters information is a crucial strategy to understand the mechanisms of heat tolerance while breeding heat tolerant dairy cattle adapted to future climatic conditions. Thus, selection for thermotolerant dairy cattle is feasible.
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Affiliation(s)
- Vincent Habimana
- Department of Animal, Aquaculture and Range Sciences, Sokoine University of Agriculture, Morogoro, Tanzania.,SACIDS Foundation for One Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania.,International Livestock Research Institute (ILRI), Nairobi, Kenya
| | | | - Athumani Shabani Nguluma
- Department of Animal, Aquaculture and Range Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | | | - Gota Morota
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | | | - Raphael Mrode
- International Livestock Research Institute (ILRI), Nairobi, Kenya
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Alia AO, Jeon S, Popovic J, Salvo MA, Sadleir KR, Vassar R, Cuddy LK. Aberrant glial activation and synaptic defects in CaMKIIα-iCre and nestin-Cre transgenic mouse models. Sci Rep 2022; 12:22099. [PMID: 36543864 PMCID: PMC9772212 DOI: 10.1038/s41598-022-26671-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Current scientific research is driven by the ability to manipulate gene expression by utilizing the Cre/loxP system in transgenic mouse models. However, artifacts in Cre-driver mouse lines that introduce undesired effects and confound results are increasingly being reported. Here, we show aberrant neuroinflammation and synaptic changes in two widely used Cre-driver mouse models. Neuroinflammation in CaMKIIα-iCre mice was characterized by the activation and proliferation of microglia and astrocytes in synaptic layers of the hippocampus. Increased GFAP and Iba1 levels were observed in hippocampal brain regions of 4-, 8- and 22-month-old CaMKIIα-iCre mice compared to WT littermates. Synaptic changes in NMDAR, AMPAR, PSD95 and phosphorylated CaMKIIα became apparent in 8-month-old CaMKIIα-iCre mice but were not observed in 4-month-old CaMKIIα-iCre mice. Synaptophysin and synaptoporin were unchanged in CaMKIIα-iCre compared to WT mice, suggesting that synaptic alterations may occur in excitatory postsynaptic regions in which iCre is predominantly expressed. Finally, hippocampal volume was reduced in 22-month-old CaMKIIα-iCre mice compared to WT mice. We tested the brains of mice of additional common Cre-driver mouse models for neuroinflammation; the nestin-Cre mouse model showed synaptic changes and astrocytosis marked by increased GFAP+ astrocytes in cortical and hippocampal regions, while the original CaMKIIα-Cre T29-1 strain was comparable to WT mice. The mechanisms underlying abnormal neuroinflammation in nestin-Cre and CaMKIIα-iCre are unknown but may be associated with high levels of Cre expression. Our findings are critical to the scientific community and demonstrate that the correct Cre-driver controls must be included in all studies using these mice.
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Affiliation(s)
- Alia O. Alia
- grid.16753.360000 0001 2299 3507The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Sohee Jeon
- grid.16753.360000 0001 2299 3507The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Jelena Popovic
- grid.16753.360000 0001 2299 3507The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Miranda A. Salvo
- grid.16753.360000 0001 2299 3507The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Katherine R. Sadleir
- grid.16753.360000 0001 2299 3507The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Robert Vassar
- grid.16753.360000 0001 2299 3507The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA ,grid.16753.360000 0001 2299 3507Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Leah K. Cuddy
- grid.16753.360000 0001 2299 3507The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
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12
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Kaare M, Jayaram M, Jagomäe T, Singh K, Kilk K, Mikheim K, Leevik M, Leidmaa E, Varul J, Nõmm H, Rähn K, Visnapuu T, Plaas M, Lilleväli K, Schäfer MKE, Philips MA, Vasar E. Depression-Associated Negr1 Gene-Deficiency Induces Alterations in the Monoaminergic Neurotransmission Enhancing Time-Dependent Sensitization to Amphetamine in Male Mice. Brain Sci 2022; 12. [PMID: 36552158 DOI: 10.3390/brainsci12121696] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
In GWAS studies, the neural adhesion molecule encoding the neuronal growth regulator 1 (NEGR1) gene has been consistently linked with both depression and obesity. Although the linkage between NEGR1 and depression is the strongest, evidence also suggests the involvement of NEGR1 in a wide spectrum of psychiatric conditions. Here we show the expression of NEGR1 both in tyrosine- and tryptophan hydroxylase-positive cells. Negr1-/- mice show a time-dependent increase in behavioral sensitization to amphetamine associated with increased dopamine release in both the dorsal and ventral striatum. Upregulation of transcripts encoding dopamine and serotonin transporters and higher levels of several monoamines and their metabolites was evident in distinct brain areas of Negr1-/- mice. Chronic (23 days) escitalopram-induced reduction of serotonin and dopamine turnover is enhanced in Negr1-/- mice, and escitalopram rescued reduced weight of hippocampi in Negr1-/- mice. The current study is the first to show alterations in the brain monoaminergic systems in Negr1-deficient mice, suggesting that monoaminergic neural circuits contribute to both depressive and obesity-related phenotypes linked to the human NEGR1 gene.
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13
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Wu SS, Lee H, Szép-Bakonyi R, Colozza G, Boese A, Gert KR, Hallay N, Lee JH, Kim J, Zhu Y, Linssen MM, Pilat-Carotta S, Hohenstein P, Theussl HC, Pauli A, Koo BK. SCON-a Short Conditional intrON for conditional knockout with one-step zygote injection. Exp Mol Med 2022; 54:2188-99. [PMID: 36494589 DOI: 10.1038/s12276-022-00891-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/02/2022] [Indexed: 12/14/2022] Open
Abstract
The generation of conditional alleles using CRISPR technology is still challenging. Here, we introduce a Short Conditional intrON (SCON, 189 bp) that enables the rapid generation of conditional alleles via one-step zygote injection. In this study, a total of 13 SCON mouse lines were successfully generated by 2 different laboratories. SCON has conditional intronic functions in various vertebrate species, and its target insertion is as simple as CRISPR/Cas9-mediated gene tagging.
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14
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Chua D, Low ZS, Cheam GX, Ng AS, Tan NS. Utility of Human Relevant Preclinical Animal Models in Navigating NAFLD to MAFLD Paradigm. Int J Mol Sci 2022; 23:ijms232314762. [PMID: 36499091 PMCID: PMC9737809 DOI: 10.3390/ijms232314762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/15/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Fatty liver disease is an emerging contributor to disease burden worldwide. The past decades of work established the heterogeneous nature of non-alcoholic fatty liver disease (NAFLD) etiology and systemic contributions to the pathogenesis of the disease. This called for the proposal of a redefinition in 2020 to that of metabolic dysfunction-associated fatty liver disease (MAFLD) to better reflect the current understanding of the disease. To date, several clinical cohort studies comparing NAFLD and MAFLD hint at the relevancy of the new nomenclature in enriching for patients with more severe hepatic injury and extrahepatic comorbidities. However, the underlying systemic pathogenesis is still not fully understood. Preclinical animal models have been imperative in elucidating key biological mechanisms in various contexts, including intrahepatic disease progression, interorgan crosstalk and systemic dysregulation. Furthermore, they are integral in developing novel therapeutics against MAFLD. However, substantial contextual variabilities exist across different models due to the lack of standardization in several aspects. As such, it is crucial to understand the strengths and weaknesses of existing models to better align them to the human condition. In this review, we consolidate the implications arising from the change in nomenclature and summarize MAFLD pathogenesis. Subsequently, we provide an updated evaluation of existing MAFLD preclinical models in alignment with the new definitions and perspectives to improve their translational relevance.
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Affiliation(s)
- Damien Chua
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Singapore 308232, Singapore
- Correspondence: (D.C.); (N.S.T.); Tel.: +65-63162941 (N.S.T.); Fax: +65-67913856 (N.S.T.)
| | - Zun Siong Low
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Singapore 308232, Singapore
| | - Guo Xiang Cheam
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Aik Seng Ng
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Nguan Soon Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Singapore 308232, Singapore
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore 637551, Singapore
- Correspondence: (D.C.); (N.S.T.); Tel.: +65-63162941 (N.S.T.); Fax: +65-67913856 (N.S.T.)
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15
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Fogarty MJ, Khurram OU, Mantilla CB, Sieck GC. Brain derived neurotrophic factor/tropomyosin related kinase B signaling impacts diaphragm neuromuscular transmission in a novel rat chemogenetic model. Front Cell Neurosci 2022; 16:1025463. [PMID: 36385943 PMCID: PMC9650098 DOI: 10.3389/fncel.2022.1025463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/12/2022] [Indexed: 11/29/2022] Open
Abstract
The neuromuscular junction (NMJ) mediates neural control of skeletal muscle fibers. Neurotrophic signaling, specifically brain derived neurotrophic factor (BDNF) acting through its high-affinity tropomyosin related kinase B (TrkB) receptor is known to improve neuromuscular transmission. BDNF/TrkB signaling also maintains the integrity of antero- and retrograde communication between the motor neuron soma, its distal axons and pre-synaptic terminals and influences neuromuscular transmission. In this study, we employed a novel rat chemogenetic mutation (TrkB F616), in which a 1-naphthylmethyl phosphoprotein phosphatase 1 (1NMPP1) sensitive knock-in allele allowed specific, rapid and sustained inhibition of TrkB kinase activity. In adult female and male TrkB F616 rats, treatment with either 1NMPP1 (TrkB kinase inhibition) or DMSO (vehicle) was administered in drinking water for 14 days. To assess the extent of neuromuscular transmission failure (NMTF), diaphragm muscle isometric force evoked by nerve stimulation at 40 Hz (330 ms duration trains repeated each s) was compared to isometric forces evoked by superimposed direct muscle stimulation (every 15 s). Chronic TrkB kinase inhibition (1NMPP1 group) markedly worsened NMTF compared to vehicle controls. Acute BDNF treatment did not rescue NMTF in the 1NMPP1 group. Chronic TrkB kinase inhibition did not affect the apposition of pre-synaptic terminals (labeled with synaptophysin) and post-synaptic endplates (labeled with α-Bungarotoxin) at diaphragm NMJs. We conclude that inhibition of BDNF/TrkB signaling in TrkB F616 rats disrupts diaphragm neuromuscular transmission in a similar manner to TrkB F616A mice, likely via a pre-synaptic mechanism independent of axonal branch point failure.
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Affiliation(s)
- Matthew J. Fogarty
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, United States
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
| | - Obaid U. Khurram
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, United States
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
| | - Carlos B. Mantilla
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, United States
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
| | - Gary C. Sieck
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, United States
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
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16
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Mann JM, Wei C, Chen C. How genetic defects in piRNA trimming contribute to male infertility. Andrology 2022. [PMID: 36263612 PMCID: PMC10115909 DOI: 10.1111/andr.13324] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/25/2022] [Accepted: 10/10/2022] [Indexed: 11/27/2022]
Abstract
In germ cells, small non-coding PIWI-interacting RNAs (piRNAs) work to silence harmful transposons to maintain genomic stability and regulate gene expression to ensure fertility. However, these piRNAs must undergo a series of steps during biogenesis to be properly loaded onto PIWI proteins and reach the correct nucleotide length. This review is focused on what we are learning about a crucial step in this process, piRNA trimming, in which pre-piRNAs are shortened to final lengths of 21-35 nucleotides. Recently, the 3'-5' exonuclease trimmer has been identified in various models as PNLDC1/PARN-1. Mutations of the piRNA trimmers in vivo lead to increased transposon expression, elevated levels of untrimmed pre-piRNAs, decreased piRNA stability, and male infertility. Here, we will discuss the role of piRNA trimmers in piRNA biogenesis and function, describe consequences of piRNA trimmer mutations using mammalian models and human patients, and examine future avenues of piRNA trimming-related study for clinical advancements for male infertility.
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Affiliation(s)
- Jeffrey M Mann
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
| | - Chao Wei
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
| | - Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA.,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA.,Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, Michigan, USA
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17
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Ma L, Li X, Liu C, Yan W, Ma J, Petersen RB, Peng A, Huang K. Modelling Parkinson's Disease in C. elegans: Strengths and Limitations. Curr Pharm Des 2022; 28:3033-3048. [PMID: 36111767 DOI: 10.2174/1381612828666220915103502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/08/2022] [Indexed: 01/28/2023]
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease that affects the motor system and progressively worsens with age. Current treatment options for PD mainly target symptoms, due to our limited understanding of the etiology and pathophysiology of PD. A variety of preclinical models have been developed to study different aspects of the disease. The models have been used to elucidate the pathogenesis and for testing new treatments. These models include cell models, non-mammalian models, rodent models, and non-human primate models. Over the past few decades, Caenorhabditis elegans (C. elegans) has been widely adopted as a model system due to its small size, transparent body, short generation time and life cycle, fully sequenced genome, the tractability of genetic manipulation and suitability for large scale screening for disease modifiers. Here, we review studies using C. elegans as a model for PD and highlight the strengths and limitations of the C. elegans model. Various C. elegans PD models, including neurotoxin-induced models and genetic models, are described in detail. Moreover, met.
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Affiliation(s)
- Liang Ma
- Department of Pharmacy, Wuhan Mental Health Center, Wuhan, China.,Department of Pharmacy, Wuhan Hospital for Psychotherapy, Wuhan, China
| | - Xi Li
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chengyu Liu
- Department of Transfusion Medicine, Wuhan Hospital of Traditional Chinese and Western Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wanyao Yan
- Department of Pharmacy, Wuhan Fourth Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinlu Ma
- Human Resources Department, Wuhan Mental Health Center, Wuhan, China.,Human Resources Department, Wuhan Hospital for Psychotherapy, Wuhan, China
| | - Robert B Petersen
- Foundational Sciences, Central Michigan University College of Medicine, Mount Pleasant, MI, USA
| | - Anlin Peng
- Department of Pharmacy, The Third Hospital of Wuhan, Tongren Hospital of Wuhan University, Wuhan, China
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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18
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Gabriel GC, Devine WA, Redel BK, Whitworth KM, Samuel M, Spate LD, Cecil RF, Prather RS, Wu YL, Wells KD, Lo CW. Profiling development of abdominal organs in the pig. Sci Rep 2022; 12:16245. [PMID: 36171243 DOI: 10.1038/s41598-022-19960-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
The pig is an ideal model system for studying human development and disease due to its similarities to human anatomy, physiology, size, and genome. Further, advances in CRISPR gene editing have made genetically engineered pigs viable models for the study of human pathologies and congenital anomalies. However, a detailed atlas illustrating pig development is necessary for identifying and modeling developmental defects. Here we describe normal development of the pig abdominal system and show examples of congenital defects that can arise in CRISPR gene edited SAP130 mutant pigs. Normal pigs at different gestational ages from day 20 (D20) to term were examined and the configuration of the abdominal organs was studied using 3D histological reconstructions with episcopic confocal microscopy, magnetic resonance imaging (MRI) and necropsy. This revealed prominent mesonephros, a transient embryonic organ present only during embryogenesis, at D20, while the developing metanephros that will form the permanent kidney are noted at D26. By D64 the mesonephroi are absent and only the metanephroi remain. The formation of the liver and pancreas was observed by D20 and complete by D30 and D35 respectively. The spleen and adrenal glands are first identified at D26 and completed by D42. The developing bowel and the gonads are identified at D20. The bowel appears completely rotated by D42, and testes in the male were descended at D64. This atlas and the methods used are excellent tools for identifying developmental pathologies of the abdominal organs in the pig at different stages of development.
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19
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Winkler L, Jimenez M, Zimmer JT, Williams A, Simon MD, Dimitrova N. Functional elements of the cis-regulatory lincRNA-p21. Cell Rep 2022; 39:110687. [PMID: 35443176 DOI: 10.1016/j.celrep.2022.110687] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 02/10/2022] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
The p53-induced long noncoding RNA (lncRNA) lincRNA-p21 is proposed to act in cis to promote p53-dependent expression of the neighboring cell cycle gene, Cdkn1a/p21. The molecular mechanism through which the transcribed lincRNA-p21 regulatory locus activates p21 expression remains poorly understood. To elucidate the functional elements of cis-regulation, we generate a series of genetic models that disrupt DNA regulatory elements, the transcription of lincRNA-p21, or the accumulation of mature lincRNA-p21. Unexpectedly, we determine that full-length transcription, splicing, and accumulation of lincRNA-p21 are dispensable for the chromatin organization of the locus and for cis-regulation. Instead, we find that production of lincRNA-p21 through conserved regions in exon 1 of lincRNA-p21 promotes cis-activation. These findings demonstrate that the activation of nascent transcription from this lncRNA locus, but not the generation or accumulation of a mature lncRNA transcript, is necessary to enact local gene expression control.
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Affiliation(s)
- Lauren Winkler
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Maria Jimenez
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Adam Williams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Nadya Dimitrova
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA.
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20
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Lax C, Cánovas-Márquez JT, Tahiri G, Navarro E, Garre V, Nicolás FE. Genetic Manipulation in Mucorales and New Developments to Study Mucormycosis. Int J Mol Sci 2022; 23:3454. [PMID: 35408814 DOI: 10.3390/ijms23073454] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 12/04/2022] Open
Abstract
The study of the Mucoralean fungi physiology is a neglected field that the lack of effective genetic tools has hampered in the past. However, the emerging fungal infection caused by these fungi, known as mucormycosis, has prompted many researchers to study the pathogenic potential of Mucorales. The main reasons for this current attraction to study mucormycosis are its high lethality, the lack of effective antifungal drugs, and its recent increased incidence. The most contemporary example of the emergence character of mucormycosis is the epidemics declared in several Asian countries as a direct consequence of the COVID-19 pandemic. Fortunately, this pressure to understand mucormycosis and develop new treatment strategies has encouraged the blossoming of new genetic techniques and methodologies. This review describes the history of genetic manipulation in Mucorales, highlighting the development of methods and how they allowed the main genetic studies in these fungi. Moreover, we have emphasized the recent development of new genetic models to study mucormycosis, a landmark in the field that will configure future research related to this disease.
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21
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Mohamed FF, Chavez MB, de Oliveira FA, Narisawa S, Farquharson C, Millán JL, Foster BL. Perspective on Dentoalveolar Manifestations Resulting From PHOSPHO1 Loss-of-Function: A Form of Pseudohypophosphatasia? Front Dent Med 2022; 3:826387. [PMID: 36185572 PMCID: PMC9521815 DOI: 10.3389/fdmed.2022.826387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Mineralization of the skeleton occurs by several physicochemical and biochemical processes and mechanisms that facilitate the deposition of hydroxyapatite (HA) in specific areas of the extracellular matrix (ECM). Two key phosphatases, phosphatase, orphan 1 (PHOSPHO1) and tissue-non-specific alkaline phosphatase (TNAP), play complementary roles in the mineralization process. The actions of PHOSPHO1 on phosphocholine and phosphoethanolamine in matrix vesicles (MVs) produce inorganic phosphate (Pi) for the initiation of HA mineral formation within MVs. TNAP hydrolyzes adenosine triphosphate (ATP) and the mineralization inhibitor, inorganic pyrophosphate (PPi), to generate Pi that is incorporated into MVs. Genetic mutations in the ALPL gene-encoding TNAP lead to hypophosphatasia (HPP), characterized by low circulating TNAP levels (ALP), rickets in children and/or osteomalacia in adults, and a spectrum of dentoalveolar defects, the most prevalent being lack of acellular cementum leading to premature tooth loss. Given that the skeletal manifestations of genetic ablation of the Phospho1 gene in mice resemble many of the manifestations of HPP, we propose that Phospho1 gene mutations may underlie some cases of "pseudo-HPP" where ALP may be normal to subnormal, but ALPL mutation(s) have not been identified. The goal of this perspective article is to compare and contrast the loss-of-function effects of TNAP and PHOSPHO1 on the dentoalveolar complex to predict the likely dental phenotype in humans that may result from PHOSPHO1 mutations. Potential cases of pseudo-HPP associated with PHOSPHO1 mutations may resist diagnosis, and the dental manifestations could be a key criterion for consideration.
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Affiliation(s)
- Fatma F. Mohamed
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, United States
| | - Michael B. Chavez
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, United States
| | - Flavia Amadeu de Oliveira
- Sanford Children’s Health Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Sonoko Narisawa
- Sanford Children’s Health Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Colin Farquharson
- The Royal (Dick) School of Veterinary Studies (RDSVS), The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - José Luis Millán
- Sanford Children’s Health Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Brian L. Foster
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, United States,,Correspondence: Brian L. Foster,
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22
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Radisavljevic N, Cirstea M, Bauer K, Lo C, Metcalfe-Roach A, Bozorgmehr T, Bar-Yoseph H, Brett Finlay B. Effects of Gut Microbiota Alterations on Motor, Gastrointestinal, and Behavioral Phenotype in a Mouse Model of Parkinson's Disease. J Parkinsons Dis 2022; 12:1479-1495. [PMID: 35599496 DOI: 10.3233/jpd-223165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Parkinson's disease (PD) is a multi-system disorder consisting of not only classic motor symptoms but also a variety of non-motor symptoms including gastrointestinal (GI) dysfunction and mood disorders. The gut microbiota has been suggested to play a role in modulating PD motor and non-motor features, although the causality and mechanisms behind these proposed interactions remains largely understudied. OBJECTIVE In this study, we aimed to provide in-depth characterization of an established mouse model of PD (transgenic (TG) SNCA A53T) and experimentally address how changes to the gut microbiota impact the PD-like phenotype. METHODS We profiled the PD-like phenotype of transgenic mice through a panel of motor, GI, and behavioral tests. We then investigated how antibiotic treatment or gut microbial community transfer (via cohousing with wild-type mice) impacted the PD-like phenotype. RESULTS We found that this mouse model demonstrated early (6 weeks of age) motor symptoms when compared to a wild-type control mouse strain. Transgenic mice also exhibited early GI dysfunction, as well as behavioral alterations, including reduced anxiety-like behavior, and increased depression-like and apathy-like behavior. Compared to wild-type mice, the transgenic fecal microbiota was less diverse and compositionally distinct. Interestingly, drastic alterations to the gut microbiota, through antibiotic treatment or cohousing with wild-type mice, had a minimal effect on the motor, GI, and behavioral phenotype of transgenic mice. CONCLUSION We concluded that this mouse model effectively recapitulates motor and non-motor features of PD; however, the gut microbiota appears to exhibit a minor impact on the pathophysiology of this PD model.
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Affiliation(s)
- Nina Radisavljevic
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Mihai Cirstea
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Kylynda Bauer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Christine Lo
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Avril Metcalfe-Roach
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Tahereh Bozorgmehr
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Haggai Bar-Yoseph
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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23
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Lima S, Sousa N, Patrício P, Pinto L. The underestimated sex: a review on female animal models of depression. Neurosci Biobehav Rev 2021:S0149-7634(21)00569-8. [PMID: 34953920 DOI: 10.1016/j.neubiorev.2021.12.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 01/19/2023]
Abstract
Major depression (MD) is the most common psychiatric disorder, predicted to affect around 264 million people worldwide. Although the etiology of depression remains elusive, the interplay between genetics and environmental factors, such as early life events, stress, exposure to drugs and health problems appears to underlie its development. Whereas depression is twice more prevalent in women than in men, most preclinical studies are performed in male rodents. In fact, females' physiology and reproductive experience are associated with changes to brain, behavior and endocrine profiles that may influence both stress, an important precipitating factor for depression, and response to treatment. These specificities emphasize the need to choose the most suitable models and readouts in order to better understand the pathophysiological mechanisms of depression in females. With this review, we aim to provide an overview of female animal models of depression highlighting the major differences between models, regarding behavioral, physiological, and molecular readouts, but also the major gaps in research, attending to the role of etiological factors, protocol variability and sex.
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24
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Rouco R, Bompadre O, Rauseo A, Fazio O, Peraldi R, Thorel F, Andrey G. Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer. Nat Commun 2021; 12:7235. [PMID: 34903763 DOI: 10.1038/s41467-021-27492-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/24/2021] [Indexed: 11/17/2022] Open
Abstract
Developmental genes are frequently controlled by multiple enhancers sharing similar specificities. As a result, deletions of such regulatory elements have often failed to reveal their full function. Here, we use the Pitx1 testbed locus to characterize in detail the regulatory and cellular identity alterations following the deletion of one of its enhancers (Pen). By combining single cell transcriptomics and an in-embryo cell tracing approach, we observe an increased fraction of Pitx1 non/low-expressing cells and a decreased fraction of Pitx1 high-expressing cells. We find that the over-representation of Pitx1 non/low-expressing cells originates from a failure of the Pitx1 locus to coordinate enhancer activities and 3D chromatin changes. This locus mis-activation induces a localized heterochrony and a concurrent loss of irregular connective tissue, eventually leading to a clubfoot phenotype. This data suggests that, in some cases, redundant enhancers may be used to locally enforce a robust activation of their host regulatory landscapes.
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25
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van Drunen L, Dobbelaar S, van der Cruijsen R, van der Meulen M, Achterberg M, Wierenga LM, Crone EA. The nature of the self: Neural analyses and heritability estimates of self-evaluations in middle childhood. Hum Brain Mapp 2021; 42:5609-5625. [PMID: 34477265 PMCID: PMC8559501 DOI: 10.1002/hbm.25641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 08/10/2021] [Accepted: 08/15/2021] [Indexed: 01/03/2023] Open
Abstract
How neural correlates of self-concept are influenced by environmental versus genetic factors is currently not fully understood. We investigated heritability estimates of behavioral and neural correlates of self-concept in middle childhood since this phase is an important time window for taking on new social roles in academic and social contexts. To do so, a validated self-concept fMRI task was applied in a twin sample of 345 participants aged between 7 and 9 years. In the self-concept condition, participants were asked to indicate whether academic and social traits applied to them whereas the control condition required trait categorization. The self-processing activation analyses (n = 234) revealed stronger medial prefrontal cortex (mPFC) activation for self than for control conditions. This effect was more pronounced for social-self than academic self-traits, whereas stronger dorsolateral prefrontal cortex (DLPFC) activation was observed for academic versus social self-evaluations. Behavioral genetic modeling (166 complete twin pairs) revealed that 25-52% of the variation in academic self-evaluations was explained by genetic factors, whereas 16-49% of the variation in social self-evaluations was explained by shared environmental factors. Neural genetic modeling (91 complete twin pairs) for variation in mPFC and anterior prefrontal cortex (PFC) activation for academic self-evaluations confirmed genetic and unique environmental influences, whereas anterior PFC activation for social self-evaluations was additionally influenced by shared environmental influences. This indicates that environmental context possibly has a larger impact on the behavioral and neural correlates of social self-concept at a young age. This is the first study demonstrating in a young twin sample that self-concept depends on both genetic and environmental factors, depending on the specific domain.
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Affiliation(s)
- Lina van Drunen
- Leiden Consortium of Individual Development (L-CID), Leiden, The Netherlands.,School of Social and Behavioral Sciences, Developmental Neuroscience in Society, Erasmus University Rotterdam, Rotterdam, The Netherlands.,Social and Behavioral Sciences, Developmental and Educational Psychology, Institute of Psychology, Leiden University, Leiden, The Netherlands.,Leiden Institute for Brain and Cognition (LIBC), Leiden, The Netherlands
| | - Simone Dobbelaar
- Leiden Consortium of Individual Development (L-CID), Leiden, The Netherlands.,School of Social and Behavioral Sciences, Developmental Neuroscience in Society, Erasmus University Rotterdam, Rotterdam, The Netherlands.,Social and Behavioral Sciences, Developmental and Educational Psychology, Institute of Psychology, Leiden University, Leiden, The Netherlands.,Leiden Institute for Brain and Cognition (LIBC), Leiden, The Netherlands
| | - Renske van der Cruijsen
- School of Social and Behavioral Sciences, Developmental Neuroscience in Society, Erasmus University Rotterdam, Rotterdam, The Netherlands.,Leiden Institute for Brain and Cognition (LIBC), Leiden, The Netherlands
| | - Mara van der Meulen
- Leiden Consortium of Individual Development (L-CID), Leiden, The Netherlands.,Social and Behavioral Sciences, Developmental and Educational Psychology, Institute of Psychology, Leiden University, Leiden, The Netherlands.,Leiden Institute for Brain and Cognition (LIBC), Leiden, The Netherlands
| | - Michelle Achterberg
- Leiden Consortium of Individual Development (L-CID), Leiden, The Netherlands.,School of Social and Behavioral Sciences, Developmental Neuroscience in Society, Erasmus University Rotterdam, Rotterdam, The Netherlands.,Leiden Institute for Brain and Cognition (LIBC), Leiden, The Netherlands
| | - Lara M Wierenga
- Leiden Consortium of Individual Development (L-CID), Leiden, The Netherlands.,Social and Behavioral Sciences, Developmental and Educational Psychology, Institute of Psychology, Leiden University, Leiden, The Netherlands.,Leiden Institute for Brain and Cognition (LIBC), Leiden, The Netherlands
| | - Eveline A Crone
- Leiden Consortium of Individual Development (L-CID), Leiden, The Netherlands.,School of Social and Behavioral Sciences, Developmental Neuroscience in Society, Erasmus University Rotterdam, Rotterdam, The Netherlands.,Leiden Institute for Brain and Cognition (LIBC), Leiden, The Netherlands
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26
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Liu Y, Ouyang P, Zheng Y, Mi L, Zhao J, Ning Y, Guo W. A Selective Review of the Excitatory-Inhibitory Imbalance in Schizophrenia: Underlying Biology, Genetics, Microcircuits, and Symptoms. Front Cell Dev Biol 2021; 9:664535. [PMID: 34746116 PMCID: PMC8567014 DOI: 10.3389/fcell.2021.664535] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 09/27/2021] [Indexed: 12/29/2022] Open
Abstract
Schizophrenia is a chronic disorder characterized by specific positive and negative primary symptoms, social behavior disturbances and cognitive deficits (e.g., impairment in working memory and cognitive flexibility). Mounting evidence suggests that altered excitability and inhibition at the molecular, cellular, circuit and network level might be the basis for the pathophysiology of neurodevelopmental and neuropsychiatric disorders such as schizophrenia. In the past decades, human and animal studies have identified that glutamate and gamma-aminobutyric acid (GABA) neurotransmissions are critically involved in several cognitive progresses, including learning and memory. The purpose of this review is, by analyzing emerging findings relating to the balance of excitatory and inhibitory, ranging from animal models of schizophrenia to clinical studies in patients with early onset, first-episode or chronic schizophrenia, to discuss how the excitatory-inhibitory imbalance may relate to the pathophysiology of disease phenotypes such as cognitive deficits and negative symptoms, and highlight directions for appropriate therapeutic strategies.
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Affiliation(s)
- Yi Liu
- National Clinical Research Center on Mental Disorders and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China.,Department of Psychiatry, The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, China
| | - Pan Ouyang
- National Clinical Research Center on Mental Disorders and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yingjun Zheng
- Department of Psychiatry, The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, China
| | - Lin Mi
- Department of Psychiatry, The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jingping Zhao
- National Clinical Research Center on Mental Disorders and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yuping Ning
- Department of Psychiatry, The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, China.,The First School of Clinical Medical University, Guangzhou, China
| | - Wenbin Guo
- National Clinical Research Center on Mental Disorders and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China
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27
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Lopez-Cruz M, Beyene Y, Gowda M, Crossa J, Pérez-Rodríguez P, de los Campos G. Multi-generation genomic prediction of maize yield using parametric and non-parametric sparse selection indices. Heredity (Edinb) 2021; 127:423-432. [PMID: 34564692 PMCID: PMC8551287 DOI: 10.1038/s41437-021-00474-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 02/07/2023] Open
Abstract
Genomic prediction models are often calibrated using multi-generation data. Over time, as data accumulates, training data sets become increasingly heterogeneous. Differences in allele frequency and linkage disequilibrium patterns between the training and prediction genotypes may limit prediction accuracy. This leads to the question of whether all available data or a subset of it should be used to calibrate genomic prediction models. Previous research on training set optimization has focused on identifying a subset of the available data that is optimal for a given prediction set. However, this approach does not contemplate the possibility that different training sets may be optimal for different prediction genotypes. To address this problem, we recently introduced a sparse selection index (SSI) that identifies an optimal training set for each individual in a prediction set. Using additive genomic relationships, the SSI can provide increased accuracy relative to genomic-BLUP (GBLUP). Non-parametric genomic models using Gaussian kernels (KBLUP) have, in some cases, yielded higher prediction accuracies than standard additive models. Therefore, here we studied whether combining SSIs and kernel methods could further improve prediction accuracy when training genomic models using multi-generation data. Using four years of doubled haploid maize data from the International Maize and Wheat Improvement Center (CIMMYT), we found that when predicting grain yield the KBLUP outperformed the GBLUP, and that using SSI with additive relationships (GSSI) lead to 5-17% increases in accuracy, relative to the GBLUP. However, differences in prediction accuracy between the KBLUP and the kernel-based SSI were smaller and not always significant.
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Affiliation(s)
- Marco Lopez-Cruz
- grid.17088.360000 0001 2150 1785Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI USA ,grid.17088.360000 0001 2150 1785Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI USA
| | - Yoseph Beyene
- grid.512317.30000 0004 7645 1801Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Manje Gowda
- grid.512317.30000 0004 7645 1801Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Jose Crossa
- grid.433436.50000 0001 2289 885XBiometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), Mexico, Mexico ,grid.418752.d0000 0004 1795 9752Colegio de Postgraduados, Montecillos, Edo. de México, Mexico
| | - Paulino Pérez-Rodríguez
- grid.418752.d0000 0004 1795 9752Colegio de Postgraduados, Montecillos, Edo. de México, Mexico
| | - Gustavo de los Campos
- grid.17088.360000 0001 2150 1785Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI USA ,grid.17088.360000 0001 2150 1785Department of Statistics and Probability, Michigan State University, East Lansing, MI USA ,grid.17088.360000 0001 2150 1785Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI USA
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28
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Rehman AU, Dang T, Qamar S, Ilyas A, Fatema R, Kafle M, Hussain Z, Masood S, Iqbal S, Shahzad K. Revisiting Plant Heterosis-From Field Scale to Molecules. Genes (Basel) 2021; 12:genes12111688. [PMID: 34828294 PMCID: PMC8619659 DOI: 10.3390/genes12111688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 11/21/2022] Open
Abstract
Heterosis refers to the increase in biomass, stature, fertility, and other characters that impart superior performance to the F1 progeny over genetically diverged parents. The manifestation of heterosis brought an economic revolution to the agricultural production and seed sector in the last few decades. Initially, the idea was exploited in cross-pollinated plants, but eventually acquired serious attention in self-pollinated crops as well. Regardless of harvesting the benefits of heterosis, a century-long discussion is continued to understand the underlying basis of this phenomenon. The massive increase in knowledge of various fields of science such as genetics, epigenetics, genomics, proteomics, and metabolomics persistently provide new insights to understand the reasons for the expression of hybrid vigor. In this review, we have gathered information ranging from classical genetic studies, field experiments to various high-throughput omics and computational modelling studies in order to understand the underlying basis of heterosis. The modern-day science has worked significantly to pull off our understanding of heterosis yet leaving open questions that requires further research and experimentation. Answering these questions would possibly equip today’s plant breeders with efficient tools and accurate choices to breed crops for a sustainable future.
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Affiliation(s)
- Attiq ur Rehman
- Horticulture Technologies, Production Systems Unit, Natural Resources Institute (Luke), Toivonlinnantie 518, 21500 Piikkiö, Finland;
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, The University of Helsinki, 00790 Helsinki, Finland;
| | - Trang Dang
- Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
- Correspondence:
| | - Shanzay Qamar
- Department of Agricultural Biotechnology, National Institute of Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Science, Faisalabad 38000, Pakistan;
| | - Amina Ilyas
- Department of Botany, Government College University, Lahore 54000, Pakistan;
| | - Reemana Fatema
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), SE-230 53 Alnarp, Sweden;
- Department of Seed Science and Technology, Ege University, Bornova, Izmir 35100, Turkey
| | - Madan Kafle
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, The University of Helsinki, 00790 Helsinki, Finland;
| | - Zawar Hussain
- Environmental and Plant Biology Department, Ohio University, Athens, OH 45701, USA;
| | - Sara Masood
- University Institute of Diet and Nutritional Sciences (UIDNS), Faculty of Allied Health Sciences, University of Lahore, Lahore 54000, Pakistan;
| | - Shehyar Iqbal
- IMPLANTEUS Graduate School, Avignon Université, 84000 Avignon, France;
| | - Khurram Shahzad
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur 22620, Pakistan;
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29
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Winkler L, Dimitrova N. A mechanistic view of long noncoding RNAs in cancer. Wiley Interdiscip Rev RNA 2021; 13:e1699. [PMID: 34668345 PMCID: PMC9016092 DOI: 10.1002/wrna.1699] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/23/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as important modulators of a wide range of biological processes in normal and disease states. In particular, lncRNAs have garnered significant interest as novel players in the molecular pathology of cancer, spurring efforts to define the functions, and elucidate the mechanisms through which cancer‐associated lncRNAs operate. In this review, we discuss the prevalent mechanisms employed by lncRNAs, with a critical assessment of the methodologies used to determine each molecular function. We survey the abilities of cancer‐associated lncRNAs to enact diverse trans functions throughout the nucleus and in the cytoplasm and examine the local roles of cis‐acting lncRNAs in modulating the expression of neighboring genes. In linking lncRNA functions and mechanisms to their roles in cancer biology, we contend that a detailed molecular understanding of lncRNA functionality is key to elucidating their contributions to tumorigenesis and to unlocking their therapeutic potential. This article is categorized under:Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Lauren Winkler
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Nadya Dimitrova
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
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30
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Kaare M, Mikheim K, Lilleväli K, Kilk K, Jagomäe T, Leidmaa E, Piirsalu M, Porosk R, Singh K, Reimets R, Taalberg E, Schäfer MKE, Plaas M, Vasar E, Philips MA. High-Fat Diet Induces Pre-Diabetes and Distinct Sex-Specific Metabolic Alterations in Negr1-Deficient Mice. Biomedicines 2021; 9:1148. [PMID: 34572334 PMCID: PMC8466019 DOI: 10.3390/biomedicines9091148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 11/16/2022] Open
Abstract
In the large GWAS studies, NEGR1 gene has been one of the most significant gene loci for body mass phenotype. The purpose of the current study was to clarify the role of NEGR1 in the maintenance of systemic metabolism, including glucose homeostasis, by using both male and female Negr1-/- mice receiving a standard or high fat diet (HFD). We found that 6 weeks of HFD leads to higher levels of blood glucose in Negr1-/- mice. In the glucose tolerance test, HFD induced phenotype difference only in male mice; Negr1-/- male mice displayed altered glucose tolerance, accompanied with upregulation of circulatory branched-chain amino acids (BCAA). The general metabolomic profile indicates that Negr1-/- mice are biased towards glyconeogenesis, fatty acid synthesis, and higher protein catabolism, all of which are amplified by HFD. Negr1 deficiency appears to induce alterations in the efficiency of energy storage; reduced food intake could be an attempt to compensate for the metabolic challenge present in the Negr1-/- males, particularly during the HFD exposure. Our results suggest that the presence of functional Negr1 allows male mice to consume more HFD and prevents the development of glucose intolerance, liver steatosis, and excessive weight gain.
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Affiliation(s)
- Maria Kaare
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (K.M.); (K.L.); (T.J.); (M.P.); (K.S.); (E.V.); (M.-A.P.)
- Center of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (K.K.); (R.P.); (E.T.)
| | - Kaie Mikheim
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (K.M.); (K.L.); (T.J.); (M.P.); (K.S.); (E.V.); (M.-A.P.)
- Center of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (K.K.); (R.P.); (E.T.)
| | - Kersti Lilleväli
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (K.M.); (K.L.); (T.J.); (M.P.); (K.S.); (E.V.); (M.-A.P.)
- Center of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (K.K.); (R.P.); (E.T.)
| | - Kalle Kilk
- Center of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (K.K.); (R.P.); (E.T.)
- Institute of Biomedicine and Translational Medicine, Department of Biochemistry, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia
| | - Toomas Jagomäe
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (K.M.); (K.L.); (T.J.); (M.P.); (K.S.); (E.V.); (M.-A.P.)
- Center of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (K.K.); (R.P.); (E.T.)
- Institute of Biomedicine and Translational Medicine, Laboratory Animal Center, University of Tartu, 14B Ravila Street, 50411 Tartu, Estonia; (R.R.); (M.P.)
| | - Este Leidmaa
- Institute of Molecular Psychiatry, Medical Faculty, University of Bonn, 53129 Bonn, Germany;
| | - Maria Piirsalu
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (K.M.); (K.L.); (T.J.); (M.P.); (K.S.); (E.V.); (M.-A.P.)
- Center of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (K.K.); (R.P.); (E.T.)
| | - Rando Porosk
- Center of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (K.K.); (R.P.); (E.T.)
- Institute of Biomedicine and Translational Medicine, Department of Biochemistry, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia
| | - Katyayani Singh
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (K.M.); (K.L.); (T.J.); (M.P.); (K.S.); (E.V.); (M.-A.P.)
- Center of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (K.K.); (R.P.); (E.T.)
| | - Riin Reimets
- Institute of Biomedicine and Translational Medicine, Laboratory Animal Center, University of Tartu, 14B Ravila Street, 50411 Tartu, Estonia; (R.R.); (M.P.)
| | - Egon Taalberg
- Center of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (K.K.); (R.P.); (E.T.)
- Institute of Biomedicine and Translational Medicine, Department of Biochemistry, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia
| | - Michael K. E. Schäfer
- Department of Anesthesiology, Focus Program Translational Neurosciences, Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany;
| | - Mario Plaas
- Institute of Biomedicine and Translational Medicine, Laboratory Animal Center, University of Tartu, 14B Ravila Street, 50411 Tartu, Estonia; (R.R.); (M.P.)
| | - Eero Vasar
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (K.M.); (K.L.); (T.J.); (M.P.); (K.S.); (E.V.); (M.-A.P.)
- Center of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (K.K.); (R.P.); (E.T.)
| | - Mari-Anne Philips
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (K.M.); (K.L.); (T.J.); (M.P.); (K.S.); (E.V.); (M.-A.P.)
- Center of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (K.K.); (R.P.); (E.T.)
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Abstract
Parkinson’s disease (PD) is a common chronic progressive multifactorial neurodegenerative disease. In most cases, PD develops as a sporadic idiopathic disease. However, in 10%–15% of all patients, Mendelian inheritance of the disease is observed in an autosomal dominant or autosomal recessive manner. To date, mutations in seven genes have been convincingly confirmed as causative in typical familial forms of PD, i.e., SNCA, LRRK2, VPS35, PRKN, PINK1, GBA, and DJ-1. Family and genome-wide association studies have also identified a number of candidate disease genes and a common genetic variability at 90 loci has been linked to risk for PD. The analysis of the biological function of both proven and candidate genes made it possible to conclude that mitochondrial dysfunction, lysosomal dysfunction, impaired exosomal transport, and immunological processes can play important roles in the development of the pathological process of PD. The mechanisms of initiation of the pathological process and its earliest stages remain unclear. The study of the early stages of the disease (before the first motor symptoms appear) is extremely complicated by the long preclinical period. In addition, at present, the possibility of performing complex biochemical and molecular biological studies familial forms of PD is limited. However, in this case, the analysis of the state of the central nervous system can only be assessed by indirect signs, such as the level of metabolites in the cerebrospinal fluid, peripheral blood, and other biological fluids. One of the potential solutions to this problem is the analysis of disease models, in which it is possible to conduct a detailed in-depth study of all aspects of the pathological process, starting from its earliest stages. Many modeling options are available currently. An analysis of studies published in the 2000s suggests that toxic models in rodents are used in the vast majority of cases. However, interesting and important data for understanding the pathogenesis of PD can be obtained from other in vivo models. Within the framework of this review, we will consider various models of PD that were created using various living organisms, from unicellular yeast (Saccharomyces cerevisiae) and invertebrate (Nematode and Drosophila) forms to various mammalian species.
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Affiliation(s)
- Maria Shadrina
- Laboratory of Molecular Genetics of Hereditary Diseases, Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Petr Slominsky
- Laboratory of Molecular Genetics of Hereditary Diseases, Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
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Chesney KL, Men H, Hankins MA, Bryda EC. The Atg16l1 gene: characterization of wild type, knock-in, and knock-out phenotypes in rats. Physiol Genomics 2021; 53:269-281. [PMID: 33818130 PMCID: PMC8285577 DOI: 10.1152/physiolgenomics.00114.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 03/08/2021] [Accepted: 03/15/2021] [Indexed: 01/08/2023] Open
Abstract
ATG16L1 is a ubiquitous autophagy gene responsible, in part, for formation of the double-membrane bound autophagosome that delivers unwanted cellular debris and intracellular pathogens to the lysosome for degradation. A single, nonsynonymous adenine to guanine polymorphism resulting in a threonine to alanine amino acid substitution (T300A) directly preceded by a caspase cleavage site (DxxD) causes an increased susceptibility to Crohn's disease (CD) in humans. The mechanism behind this increased susceptibility is still being elucidated, however, the amino acid change caused by this point mutation results in increased ATG16L1 protein sensitivity to caspase 3-mediated cleavage. To generate novel rat strains carrying genetic alterations in the rat Atg16l1 gene, we first characterized the wild-type rat gene. We identified four alternative splice variants with tissue-specific expression. Using CRISPR-Cas9 genome editing technology, we developed a knock-in rat model for the human ATG16L1 T300A CD risk polymorphism, as well as a knock-out rat model to evaluate the role of Atg16l1 in autophagy as well as its potential effect on CD susceptibility. These are the first reported rat strains with alterations of the Atg16l1 gene. Consistent with studies of the effects of human ATG16L1 polymorphisms, models exhibit morphological abnormalities in both Paneth and goblet cells, but do not develop spontaneous intestinal permeability or inflammatory bowel disease. Analysis of the gut microbiota does not show inherent differences in bacterial composition between wild-type and genetically modified animals. These Atg16l1 strains are valuable new animal models for the study of both autophagy and CD susceptibility.
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Affiliation(s)
- Kari L Chesney
- Comparative Medicine Program, College of Veterinary Medicine, University of Missouri, Columbia, Missouri
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri
| | - Hongsheng Men
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri
- Rat Resource and Research Center, University of Missouri, Columbia, Missouri
| | - Miriam A Hankins
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri
- Rat Resource and Research Center, University of Missouri, Columbia, Missouri
| | - Elizabeth C Bryda
- Comparative Medicine Program, College of Veterinary Medicine, University of Missouri, Columbia, Missouri
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri
- Rat Resource and Research Center, University of Missouri, Columbia, Missouri
- Animal Modeling Core, University of Missouri, Columbia, Missouri
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Singh M, Valecha S, Khinda R, Kumar N, Singh S, Juneja PK, Kaur T, Di Napoli M, Minhas JS, Singh P, Mastana S. Multifactorial Landscape Parses to Reveal a Predictive Model for Knee Osteoarthritis. Int J Environ Res Public Health 2021; 18:ijerph18115933. [PMID: 34073132 PMCID: PMC8199148 DOI: 10.3390/ijerph18115933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/20/2021] [Accepted: 05/28/2021] [Indexed: 12/18/2022]
Abstract
The present study attempted to investigate whether concerted contributions of significant risk variables, pro-inflammatory markers, and candidate genes translate into a predictive marker for knee osteoarthritis (KOA). The present study comprised 279 confirmed osteoarthritis patients (Kellgren and Lawrence scale ≥2) and 287 controls. Twenty SNPs within five genes (CRP, COL1A1, IL-6, VDR, and eNOS), four pro-inflammatory markers (interleukin-6 (IL-6), interleuin-1 beta (IL-1β), tumor necrosis factor alpha (TNF-α), and high sensitivity C-reactive protein (hsCRP)), along with significant risk variables were investigated. A receiver operating characteristic (ROC) curve was used to observe the predictive ability of the model for distinguishing patients with KOA. Multivariable logistic regression analysis revealed that higher body mass index (BMI), triglycerides (TG), poor sleep, IL-6, IL-1β, and hsCRP were independent predictors for KOA after adjusting for the confounding from other risk variables. Four susceptibility haplotypes for the risk of KOA, AGT, GGGGCT, AGC, and CTAAAT, were observed within CRP, IL-6, VDR, and eNOS genes, which showed their impact in recessive β(SE): 2.11 (0.76), recessive β(SE): 2.75 (0.59), dominant β(SE): 1.89 (0.52), and multiplicative modes β(SE): 1.89 (0.52), respectively. ROC curve analysis revealed the model comprising higher values of BMI, poor sleep, IL-6, and IL-1β was predictive of KOA (AUC: 0.80, 95%CI: 0.74–0.86, p < 0.001), and the strength of the predictive ability increased when susceptibility haplotypes AGC and GGGGCT were involved (AUC: 0.90, 95%CI: 0.87–0.95, p < 0.001).This study offers a predictive marker for KOA based on the risk scores of some pertinent genes and their genetic variants along with some pro-inflammatory markers and traditional risk variables.
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Affiliation(s)
- Monica Singh
- Division of Molecular Genetics, Department of Human Genetics, Punjabi University, Patiala 147002, India; (M.S.); (S.V.); (R.K.); (N.K.)
| | - Srishti Valecha
- Division of Molecular Genetics, Department of Human Genetics, Punjabi University, Patiala 147002, India; (M.S.); (S.V.); (R.K.); (N.K.)
| | - Rubanpal Khinda
- Division of Molecular Genetics, Department of Human Genetics, Punjabi University, Patiala 147002, India; (M.S.); (S.V.); (R.K.); (N.K.)
| | - Nitin Kumar
- Division of Molecular Genetics, Department of Human Genetics, Punjabi University, Patiala 147002, India; (M.S.); (S.V.); (R.K.); (N.K.)
| | - Surinderpal Singh
- Aggarwal Orthopedic Hospital, Ludhiana 141001, India; (S.S.); (P.K.J.)
| | - Pawan K. Juneja
- Aggarwal Orthopedic Hospital, Ludhiana 141001, India; (S.S.); (P.K.J.)
| | | | - Mario Di Napoli
- Neurological Service, Annunziata Hospital, Sulmona, 67039 L’Aquila, Italy;
| | - Jatinder S. Minhas
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE1 7RH, UK;
| | - Puneetpal Singh
- Division of Molecular Genetics, Department of Human Genetics, Punjabi University, Patiala 147002, India; (M.S.); (S.V.); (R.K.); (N.K.)
- Correspondence: (P.S.); (S.M.)
| | - Sarabjit Mastana
- Human Genomics Lab, School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough LE11 3TU, UK
- Correspondence: (P.S.); (S.M.)
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Du M, Bernstein R, Hoppe A, Bienefeld K. Short-term effects of controlled mating and selection on the genetic variance of honeybee populations. Heredity (Edinb) 2021; 126:733-47. [PMID: 33785894 DOI: 10.1038/s41437-021-00411-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 02/01/2023] Open
Abstract
Directional selection in a population yields reduced genetic variance due to the Bulmer effect. While this effect has been thoroughly investigated in mammals, it is poorly studied in social insects with biological peculiarities such as haplo-diploidy or the collective expression of traits. In addition to the natural adaptation to climate change, parasites, and pesticides, honeybees increasingly experience artificial selection pressure through modern breeding programs. Besides selection, many honeybee breeding schemes introduce controlled mating. We investigated which individual effects selection and controlled mating have on genetic variance. We derived formulas to describe short-term changes of genetic variance in honeybee populations and conducted computer simulations to confirm them. Thereby, we found that the changes in genetic variance depend on whether the variance is measured between queens (inheritance criterion), worker groups (selection criterion), or both (performance criterion). All three criteria showed reduced genetic variance under selection. In the selection and performance criteria, our formulas and simulations showed an increased genetic variance through controlled mating. This newly described effect counterbalanced and occasionally outweighed the Bulmer effect. It could not be observed in the inheritance criterion. A good understanding of the different notions of genetic variance in honeybees, therefore, appears crucial to interpreting population parameters correctly.
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Abstract
Cancer predisposition syndromes are rare, typically monogenic disorders that result from germline mutations that increase the likelihood of developing cancer. Although these disorders are individually rare, resulting cancers collectively represent 5-10% of all malignancies. In addition to a greater incidence of cancer, affected individuals have an earlier tumor onset and are frequently subjected to long-term multi-modal cancer screening protocols for earlier detection and initiation of treatment. In vivo models are needed to better understand tumor-driving mechanisms, tailor patient screening approaches and develop targeted therapies to improve patient care and disease prognosis. The zebrafish (Danio rerio) has emerged as a robust model for cancer research due to its high fecundity, time- and cost-efficient genetic manipulation and real-time high-resolution imaging. Tumors developing in zebrafish cancer models are histologically and molecularly similar to their human counterparts, confirming the validity of these models. The zebrafish platform supports both large-scale random mutagenesis screens to identify potential candidate/modifier genes and recently optimized genome editing strategies. These techniques have greatly increased our ability to investigate the impact of certain mutations and how these lesions impact tumorigenesis and disease phenotype. These unique characteristics position the zebrafish as a powerful in vivo tool to model cancer predisposition syndromes and as such, several have already been created, including those recapitulating Li-Fraumeni syndrome, familial adenomatous polyposis, RASopathies, inherited bone marrow failure syndromes, and several other pathogenic mutations in cancer predisposition genes. In addition, the zebrafish platform supports medium- to high-throughput preclinical drug screening to identify compounds that may represent novel treatment paradigms or even prevent cancer evolution. This review will highlight and synthesize the findings from zebrafish cancer predisposition models created to date. We will discuss emerging trends in how these zebrafish cancer models can improve our understanding of the genetic mechanisms driving cancer predisposition and their potential to discover therapeutic and/or preventative compounds that change the natural history of disease for these vulnerable children, youth and adults.
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Affiliation(s)
- Kim Kobar
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Keon Collett
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | | | - Jason N. Berman
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Pediatrics, University of Ottawa, Ottawa, ON, Canada
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Rahi V, Kumar P. Animal models of attention-deficit hyperactivity disorder (ADHD). Int J Dev Neurosci 2021; 81:107-124. [PMID: 33428802 DOI: 10.1002/jdn.10089] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/14/2020] [Accepted: 01/06/2021] [Indexed: 12/15/2022] Open
Abstract
Attention-deficit hyperactivity disorder (ADHD) is a heterogeneous neuropsychiatric disorder characterized by three primary symptoms hyperactivity, attention deficit, and impulsiveness, observed in both children and adults. In childhood, this disorder is more common in boys than in girls, and at least 75% will continue to suffer from the disorder until adulthood. Individuals with ADHD generally have poor academic, occupational, and social functioning resulting from developmentally inappropriate levels of hyperactivity and impulsivity, as well as impaired ability to maintain attention on motivationally relevant tasks. Very few drugs available in clinical practice altogether abolish the symptoms of ADHD, therefore, to find new drugs and target it is essential to understand the neuropathological, neurochemical, and genetic alterations that lead to the progression of ADHD. With this contrast, an animal study is the best approach because animal models provide relatively fast invasive manipulation, rigorous hypothesis testing, as well as it provides a better angle to understand the pathological mechanisms involved in disease progression. Moreover, animal models, especially for ADHD, serve with good predictive validity would allow the assessment and development of new therapeutic interventions, with this aim, the present review collect the various animal models on a single platform so that the research can select an appropriate model to pursue his study.
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Affiliation(s)
- Vikrant Rahi
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda, India
| | - Puneet Kumar
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda, India
- Department of Pharmacology, Central University of Punjab, Bathinda, India
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Singh P, Singh M, Khinda R, Valecha S, Kumar N, Singh S, Juneja PK, Kaur T, Mastana S. Genetic Scores of eNOS, ACE and VEGFA Genes Are Predictive of Endothelial Dysfunction Associated Osteoporosis in Postmenopausal Women. Int J Environ Res Public Health 2021; 18:972. [PMID: 33499313 DOI: 10.3390/ijerph18030972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 11/24/2022]
Abstract
The present study aimed to examine the participation and contribution of endothelial nitric oxide synthase (eNOS), angiotensin converting enzyme (ACE) and vascular endothelial growth factor (VEGFA) genes for the risk of endothelial dysfunction (ED)-associated osteoporosis risk in postmenopausal women of Punjab, India. Women with ED were categorized into women with osteoporosis (n = 346) and women without osteoporosis (n = 330). They were examined for selected SNPs within eNOS, ACE and VEGFA genes. Linear regression analysis revealed a positive association of ED with bone mineral densities (BMDs) at femoral neck (r2 = 0.78, p < 0.001) and lumbar spine (r2 = 0.24, p = 0.001) after Bonferroni correction. Three susceptibility haplotypes were exposed within eNOS (CTAAAT), ACE (ACDG) and VEGFA (GATA) genes. Bearers of CTAAAT (OR 2.43, p = 0.007), ACDG (OR 2.50, p = 0.002) and GATA (OR 2.10, p = 0.009) had substantial impact for osteoporosis after correcting the effects with traditional risk factors (TRD).With uncertainty measure (R2h) and Akaike information criterion (AIC), best fit models showed that CTAAAT manifested in multiplicative mode (β ± SE: 2.19 ± 0.86, p < 0.001), whereas ACDG (β ± SE: 1.73 ± 0.54, p = 0.001) and GATA (β ± SE: 3.07 ± 0.81, p < 0.001) expressed in dominant modes. Area under receiver operating characteristic curve using weighted risk scores (effect estimates) showed substantial strength for model comprising TRD + GATA (AUC = 0.8, p < 0.001) whereas, model comprising TRD + GATA + CTAAAT exhibited excellent ability to predict osteoporosis (AUC = 0.824, p < 0.001)
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Abstract
The understanding of the functional and structural changes occurring in the cerebral cortex and basal ganglia in Huntington's disease (HD) has benefited considerably from the generation of genetic animal models. Most studies of synaptic alterations in HD models have focused on the striatum, but a more complete picture of synaptic dysfunction in the cortico-basal ganglia-cortical loop is emerging. Here, we provide a review and analysis of current developments in the study of synaptic alterations in these areas using HD rodent models. Recent evidence indicates that cortical maldevelopment plays a role in synaptic dysfunction along the corticostriatal pathway that may have its roots in the way mutant huntingtin interacts with synaptic proteins. Furthermore, a progressive disconnection in the corticostriatal pathway leads to abnormal function engaging extrasynaptic N-methyl-D-aspartate glutamate receptors that contribute to eventual cell degeneration. In addition, biphasic increases followed by decreases in glutamate and dopamine release in the striatum could explain contrasting symptomatology in early and late stages of the disease. Changes in striatal output regions also are beginning to be examined. Finally, we highlight some therapeutic avenues aimed at rescuing synaptic dysfunction.
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Affiliation(s)
- Carlos Cepeda
- IDDRC, Jane and Terry Semel Institute for Neuroscience & Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Michael S Levine
- IDDRC, Jane and Terry Semel Institute for Neuroscience & Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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40
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Abstract
The diversity and dense interconnectivity of cells in the nervous system present a huge challenge to understanding how brains work. Recent progress toward such understanding, however, has been fuelled by the development of techniques for selectively monitoring and manipulating the function of distinct cell types-and even individual neurons-in the brains of living animals. These sophisticated techniques are fundamentally genetic and have found their greatest application in genetic model organisms, such as the fruit fly Drosophila melanogaster. Drosophila combines genetic tractability with a compact, but cell-type rich, nervous system and has been the incubator for a variety of methods of neuronal targeting. One such method, called Split Gal4, is playing an increasingly important role in mapping neural circuits in the fly. In conjunction with functional perturbations and behavioral screens, Split Gal4 has been used to characterize circuits governing such activities as grooming, aggression, and mating. It has also been leveraged to comprehensively map and functionally characterize cells composing important brain regions, such as the central complex, lateral horn, and the mushroom body-the latter being the insect seat of learning and memory. With connectomics data emerging for both the larval and adult brains of Drosophila, Split Gal4 is also poised to play an important role in characterizing neurons of interest based on their connectivity. We summarize the history and current state of the Split Gal4 method and indicate promising areas for further development or future application.
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Affiliation(s)
| | | | | | - Benjamin H. White
- Laboratory of Molecular Biology, National Institute of Mental Health, NIH, Bethesda, MD, United States
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Borrás T, Cowley DO, Asokan P, Pandya K. Generation of a Matrix Gla (Mgp) floxed mouse, followed by conditional knockout, uncovers a new Mgp function in the eye. Sci Rep 2020; 10:18583. [PMID: 33122788 PMCID: PMC7596545 DOI: 10.1038/s41598-020-75031-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 10/09/2020] [Indexed: 01/07/2023] Open
Abstract
The ability to ablate a gene in a given tissue by generating a conditional knockout (cKO) is crucial for determining its function in the targeted tissue. Such tissue-specific ablation is even more critical when the gene's conventional knockout (KO) is lethal, which precludes studying the consequences of its deletion in other tissues. Therefore, here we describe a successful strategy that generated a Matrix Gla floxed mouse (Mgp.floxed) by the CRISPR/Cas9 system, that subsequently allowed the generation of cKOs by local viral delivery of the Cre-recombinase enzyme. MGP is a well-established inhibitor of calcification gene, highly expressed in arteries' smooth muscle cells and chondrocytes. MGP is also one of the most abundant genes in the trabecular meshwork, the eye tissue responsible for maintenance of intraocular pressure (IOP) and development of Glaucoma. Our strategy entailed one-step injection of two gRNAs, Cas9 protein and a long-single-stranded-circular DNA donor vector (lsscDNA, 6.7 kb) containing two loxP sites in cis and 900-700 bp 5'/3' homology arms. Ocular intracameral injection of Mgp.floxed mice with a Cre-adenovirus, led to an Mgp.TMcKO mouse which developed elevated IOP. Our study discovered a new role for the Mgp gene as a keeper of physiological IOP in the eye.
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Affiliation(s)
- Teresa Borrás
- Department of Ophthalmology, University of North Carolina School of Medicine, 4109C Neuroscience Research Building CB 7041, 115 Mason Farm Road, Chapel Hill, NC, 27599-7041, USA.
| | - Dale O Cowley
- Animal Models Core, University of North Carolina, Chapel Hill, NC, USA
| | - Priyadarsini Asokan
- Department of Ophthalmology, University of North Carolina School of Medicine, 4109C Neuroscience Research Building CB 7041, 115 Mason Farm Road, Chapel Hill, NC, 27599-7041, USA
| | - Kumar Pandya
- Animal Models Core, University of North Carolina, Chapel Hill, NC, USA
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Naert T, Tulkens D, Edwards NA, Carron M, Shaidani NI, Wlizla M, Boel A, Demuynck S, Horb ME, Coucke P, Willaert A, Zorn AM, Vleminckx K. Maximizing CRISPR/Cas9 phenotype penetrance applying predictive modeling of editing outcomes in Xenopus and zebrafish embryos. Sci Rep 2020; 10:14662. [PMID: 32887910 PMCID: PMC7473854 DOI: 10.1038/s41598-020-71412-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/13/2020] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9 genome editing has revolutionized functional genomics in vertebrates. However, CRISPR/Cas9 edited F0 animals too often demonstrate variable phenotypic penetrance due to the mosaic nature of editing outcomes after double strand break (DSB) repair. Even with high efficiency levels of genome editing, phenotypes may be obscured by proportional presence of in-frame mutations that still produce functional protein. Recently, studies in cell culture systems have shown that the nature of CRISPR/Cas9-mediated mutations can be dependent on local sequence context and can be predicted by computational methods. Here, we demonstrate that similar approaches can be used to forecast CRISPR/Cas9 gene editing outcomes in Xenopus tropicalis, Xenopus laevis, and zebrafish. We show that a publicly available neural network previously trained in mouse embryonic stem cell cultures (InDelphi-mESC) is able to accurately predict CRISPR/Cas9 gene editing outcomes in early vertebrate embryos. Our observations can have direct implications for experiment design, allowing the selection of guide RNAs with predicted repair outcome signatures enriched towards frameshift mutations, allowing maximization of CRISPR/Cas9 phenotype penetrance in the F0 generation.
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Affiliation(s)
- Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Dieter Tulkens
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Nicole A Edwards
- Division of Developmental Biology, Perinatal Institute, and Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital, Cincinnati, USA
| | - Marjolein Carron
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Nikko-Ideen Shaidani
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Marcin Wlizla
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Annekatrien Boel
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Suzan Demuynck
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Marko E Horb
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Paul Coucke
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Andy Willaert
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Aaron M Zorn
- Division of Developmental Biology, Perinatal Institute, and Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital, Cincinnati, USA
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium.
- Cancer Research Institute Ghent, Ghent, Belgium.
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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Abstract
It has been more than a decade since the last comprehensive review of the phase-variable uropathogen-associated pyelonephritis-associated pilus (pap) genetic switch. Since then, important data have come to light, including additional factors that regulate pap expression, better characterization of H-NS regulation, the structure of the Lrp octamer in complex with pap regulatory DNA, the temperature-insensitive phenotype of a mutant lacking the acetyltransferase RimJ, evidence that key components of the regulatory machinery are acetylated, and new insights into the role of DNA binding by key regulators in shaping both the physical structure and regulatory state of the papI and papBA promoters. This review revisits pap, integrating these newer observations with older ones to produce a new model for the concerted behavior of this virulence-regulatory region.
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Affiliation(s)
- Mario Zamora
- Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, USA
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, USA
| | - Christine A Ziegler
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, USA
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de Abreu MS, C V V Giacomini A, Genario R, Fontana BD, Parker MO, Marcon L, Scolari N, Bueno B, Demin KA, Galstyan D, Kolesnikova TO, Amstislavskaya TG, Zabegalov KN, Strekalova T, Kalueff AV. Zebrafish models of impulsivity and impulse control disorders. Eur J Neurosci 2020; 52:4233-4248. [PMID: 32619029 DOI: 10.1111/ejn.14893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/25/2020] [Accepted: 06/18/2020] [Indexed: 12/22/2022]
Abstract
Impulse control disorders (ICDs) are characterized by generalized difficulty controlling emotions and behaviors. ICDs are a broad group of the central nervous system (CNS) disorders including conduct disorder, intermittent explosive, oppositional-defiant disorder, antisocial personality disorder, kleptomania, pyromania and other illnesses. Although they all share a common feature (aberrant impulsivity), their pathobiology is complex and poorly understood. There are also currently no ICD-specific therapies to treat these illnesses. Animal models are a valuable tool for studying ICD pathobiology and potential therapies. The zebrafish (Danio rerio) has become a useful model organism to study CNS disorders due to high genetic and physiological homology to mammals, and sensitivity to various pharmacological and genetic manipulations. Here, we summarize experimental models of impulsivity and ICD in zebrafish and highlight their growing translational significance. We also emphasize the need for further development of zebrafish ICD models to improve our understanding of their pathogenesis and to search for novel therapeutic treatments.
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Affiliation(s)
- Murilo S de Abreu
- Bioscience Institute, University of Passo Fundo, Passo Fundo, Brazil.,The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA
| | - Ana C V V Giacomini
- Bioscience Institute, University of Passo Fundo, Passo Fundo, Brazil.,Postgraduate Program in Environmental Sciences, University of Passo Fundo, Passo Fundo, Brazil
| | - Rafael Genario
- Bioscience Institute, University of Passo Fundo, Passo Fundo, Brazil
| | - Barbara D Fontana
- Brain and Behaviour Laboratory, School of Pharmacy and Biomedical Sciences, University of Portsmouth, UK
| | - Matthew O Parker
- Brain and Behaviour Laboratory, School of Pharmacy and Biomedical Sciences, University of Portsmouth, UK
| | - Leticia Marcon
- Bioscience Institute, University of Passo Fundo, Passo Fundo, Brazil
| | - Naiara Scolari
- Bioscience Institute, University of Passo Fundo, Passo Fundo, Brazil
| | - Barbara Bueno
- Bioscience Institute, University of Passo Fundo, Passo Fundo, Brazil
| | - Konstantin A Demin
- Institute of Experimental Medicine, Almazov National Medical Research Center, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia.,Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - David Galstyan
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Tatyana O Kolesnikova
- Institute of Experimental Medicine, Almazov National Medical Research Center, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
| | | | | | - Tatyana Strekalova
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.,School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands.,Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Würzburg, Germany.,Institute of General Pathology and Pathophysiology, University of Würzburg, Moscow, Russia
| | - Allan V Kalueff
- School of Pharmacy, Southwest University, Chongqing, China.,Laboratory of Petrochemistry, Ural Federal University, Ekaterinburg, Russia
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45
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Kamp JA, van Schendel R, Dilweg IW, Tijsterman M. BRCA1-associated structural variations are a consequence of polymerase theta-mediated end-joining. Nat Commun 2020; 11:3615. [PMID: 32680986 PMCID: PMC7368036 DOI: 10.1038/s41467-020-17455-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/01/2020] [Indexed: 12/03/2022] Open
Abstract
Failure to preserve the integrity of the genome is a hallmark of cancer. Recent studies have revealed that loss of the capacity to repair DNA breaks via homologous recombination (HR) results in a mutational profile termed BRCAness. The enzymatic activity that repairs HR substrates in BRCA-deficient conditions to produce this profile is currently unknown. We here show that the mutational landscape of BRCA1 deficiency in C. elegans closely resembles that of BRCA1-deficient tumours. We identify polymerase theta-mediated end-joining (TMEJ) to be responsible: knocking out polq-1 suppresses the accumulation of deletions and tandem duplications in brc-1 and brd-1 animals. We find no additional back-up repair in HR and TMEJ compromised animals; non-homologous end-joining does not affect BRCAness. The notion that TMEJ acts as an alternative to HR, promoting the genome alteration of HR-deficient cells, supports the idea that polymerase theta is a promising therapeutic target for HR-deficient tumours.
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Affiliation(s)
- J A Kamp
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - R van Schendel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - I W Dilweg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - M Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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46
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Chia SJ, Tan EK, Chao YX. Historical Perspective: Models of Parkinson's Disease. Int J Mol Sci 2020; 21:E2464. [PMID: 32252301 DOI: 10.3390/ijms21072464] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/30/2020] [Accepted: 03/30/2020] [Indexed: 01/02/2023] Open
Abstract
Parkinson’s disease (PD) is the most common movement disorder with motor and nonmotor signs. The current therapeutic regimen for PD is mainly symptomatic as the etio-pathophysiology has not been fully elucidated. A variety of animal models has been generated to study different aspects of the disease for understanding the pathogenesis and therapeutic development. The disease model can be generated through neurotoxin-based or genetic-based approaches in a wide range of animals such as non-human primates (NHP), rodents, zebrafish, Caenorhabditis (C.) elegans, and drosophila. Cellular-based disease model is frequently used because of the ease of manipulation and suitability for large-screen assays. In neurotoxin-induced models, chemicals such as 6-hydroxydopamine (6-OHDA), 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), rotenone, and paraquat are used to recapitulate the disease. Genetic manipulation of PD-related genes, such as α-Synuclein(SNCA), Leucine-rich repeat kinase 2 (LRRK2), Pten-Induced Kinase 1 (PINK1), Parkin(PRKN), and Protein deglycase (DJ-1) Are used in the transgenic models. An emerging model that combines both genetic- and neurotoxin-based methods has been generated to study the role of the immune system in the pathogenesis of PD. Here, we discuss the advantages and limitations of the different PD models and their utility for different research purposes.
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47
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Cabib S, Campus P, Conversi D, Orsini C, Puglisi-Allegra S. Functional and Dysfunctional Neuroplasticity in Learning to Cope with Stress. Brain Sci 2020; 10:E127. [PMID: 32102272 DOI: 10.3390/brainsci10020127] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/15/2020] [Accepted: 02/20/2020] [Indexed: 12/20/2022] Open
Abstract
In this brief review, we present evidence of the primary role of learning-associated plasticity in the development of either adaptive or maladaptive coping strategies. Successful interactions with novel stressors foster plasticity within the neural circuits supporting acquisition, consolidation, retrieval, and extinction of instrumental learning leading to development of a rich repertoire of flexible and context-specific adaptive coping responses, whereas prolonged or repeated exposure to inescapable/uncontrollable stressors fosters dysfunctional plasticity within the learning circuits leading to perseverant and inflexible maladaptive coping strategies. Finally, the results collected using an animal model of genotype-specific coping styles indicate the engagement of different molecular networks and the opposite direction of stress effects (reduced vs. enhanced gene expression) in stressed animals, as well as different behavioral alterations, in line with differences in the symptoms profile associated with post-traumatic stress disorder.
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48
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Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M Jr, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J. Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat Methods 2020; 17:481-94. [PMID: 32251396 DOI: 10.1038/s41592-020-0796-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 03/02/2020] [Indexed: 12/13/2022]
Abstract
Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.
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Craft CS, Robles H, Lorenz MR, Hilker ED, Magee KL, Andersen TL, Cawthorn WP, MacDougald OA, Harris CA, Scheller EL. Bone marrow adipose tissue does not express UCP1 during development or adrenergic-induced remodeling. Sci Rep 2019; 9:17427. [PMID: 31758074 PMCID: PMC6874537 DOI: 10.1038/s41598-019-54036-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/24/2019] [Indexed: 12/31/2022] Open
Abstract
Adipocytes within the skeleton are collectively termed bone marrow adipose tissue (BMAT). BMAT contributes to peripheral and local metabolism, however, its capacity for cell-autonomous expression of uncoupling protein 1 (UCP1), a biomarker of beige and brown adipogenesis, remains unclear. To overcome this, Ucp1-Cre was used to drive diphtheria toxin expression in cells expressing UCP1 (Ucp1Cre+/DTA+). Despite loss of brown adipose tissue, BMAT volume was not reduced in Ucp1Cre+/DTA+ mice. Comparably, in mTmG reporter mice (Ucp1Cre+/mTmG+), Ucp1-Cre expression was absent from BMAT in young (3-weeks) and mature (16-weeks) male and female mice. Further, β3-agonist stimulation failed to induce Ucp1-Cre expression in BMAT. This demonstrates that BMAT adipocytes are not UCP1-expressing beige/brown adipocytes. Thus, to identify novel and emerging roles for BMAT adipocytes in skeletal and whole-body homeostasis, we performed gene enrichment analysis of microarray data from adipose tissues of adult rabbits. Pathway analysis revealed genetic evidence for differences in BMAT including insulin resistance, decreased fatty acid metabolism, and enhanced contributions to local processes including bone mineral density through candidate genes such as osteopontin. In sum, this supports a paradigm by which BMAT adipocytes are a unique subpopulation that is specialized to support cells within the skeletal and hematopoietic niche.
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Affiliation(s)
- Clarissa S Craft
- Division of Bone and Mineral Diseases, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Cell Biology & Physiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Hero Robles
- Division of Bone and Mineral Diseases, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Madelyn R Lorenz
- Division of Bone and Mineral Diseases, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Eric D Hilker
- Division of Bone and Mineral Diseases, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Kristann L Magee
- Division of Bone and Mineral Diseases, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Thomas L Andersen
- Department of Pathology, Odense University Hospital - Department of Clinical Research & Department Molecular Medicine, University of Southern Denmark, Odense, Denmark
- Department of Forensic Medicine, Aarhus University, Aarhus, Denmark
| | - William P Cawthorn
- University/BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, Edinburgh Bioquarter, University of Edinburgh, Edinburgh, UK
| | - Ormond A MacDougald
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Charles A Harris
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Veterans Affairs St. Louis Healthcare System, John Cochran Division, St. Louis, MO, USA
| | - Erica L Scheller
- Division of Bone and Mineral Diseases, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO, USA.
- Department of Cell Biology & Physiology, Washington University School of Medicine, Saint Louis, MO, USA.
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50
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Chaudhary NS, Moore JX, Zakai NA, Judd SE, Naik RP, Limou S, Cushman M, Lange LA, Wang HE, Winkler CA, Irvin MR, Kopp JB, Gutiérrez OM. APOL1 Nephropathy Risk Alleles and Risk of Sepsis in Blacks. Clin J Am Soc Nephrol 2019; 14:1733-1740. [PMID: 31704668 PMCID: PMC6895473 DOI: 10.2215/cjn.04490419] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/30/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND OBJECTIVES apo L1 (APOL1) nephropathy risk alleles are associated with CKD in blacks. Although APOL1 has innate immune functions, little is known about the association of APOL1 genotypes with risk of infectious outcomes, such as sepsis. The objective of this study was to examine the associations of APOL1 nephropathy risk alleles with risk of sepsis in black adults. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We assessed the association of APOL1 risk alleles with incident sepsis in 10,366 black participants of the Reasons for Geographic and Racial Differences in Stroke study enrolled between 2003 and 2007 with follow-up through December 31, 2012. In Cox models adjusted for demographics, comorbid conditions, and principal components ancestry, we examined the association of APOL1 risk alleles with incident sepsis using recessive (comparing zero or one versus two risk alleles), dominant (zero versus one or two risk alleles), and additive genetic models. We also examined models stratified by diabetes and CKD status. RESULTS A total of 1320 (13%) participants had two APOL1 risk alleles, 4719 (46%) had one risk allele, and 4327 (42%) participants had zero risk alleles. A total of 306 sepsis events occurred over a median 6.5 years (interquartile range, 4.5-8.1). There were no statistically significant associations of APOL1 genotype with sepsis risk under recessive genetic models. APOL1 genotypes were associated with sepsis risk under dominant (hazard ratio, 1.55; 95% confidence interval, 1.13 to 2.11) and additive (hazard ratio per variant allele copy, 1.25; 95% confidence interval, 1.02 to 1.53) genetic models adjusted for covariates and ancestry. These associations did not vary by diabetes or CKD status (P interaction>0.10 for both). CONCLUSIONS In community-dwelling black adults, carriage of APOL1 nephropathy risk alleles are common and associated with higher risk of sepsis.
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Affiliation(s)
| | - Justin X Moore
- Departments of Epidemiology.,Division of Public Health Sciences, Department of Surgery, Washington University, St. Louis, Missouri
| | - Neil A Zakai
- Departments of Medicine and Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | | | - Rakhi P Naik
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Sophie Limou
- Nantes University, French National Institute of Health and Medical Research, Center for Research in Transplantation and Immunology, Nantes, France
| | - Mary Cushman
- Departments of Medicine and Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Leslie A Lange
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Henry E Wang
- Department of Emergency Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Cheryl A Winkler
- Basic Research Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland; and
| | | | - Jeffrey B Kopp
- Intramural Research Program, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Orlando M Gutiérrez
- Departments of Epidemiology, .,Medicine, University of Alabama at Birmingham, Birmingham, Alabama
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