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Tinker RJ, Bastarache L, Ezell K, Kobren SN, Esteves C, Rosenfeld JA, Macnamara EF, Hamid R, Cogan JD, Rinker D, Mukharjee S, Glass I, Dipple K, Phillips JA. The contribution of mosaicism to genetic diseases and de novo pathogenic variants. Am J Med Genet A 2023; 191:2482-2492. [PMID: 37246601 DOI: 10.1002/ajmg.a.63309] [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] [Received: 02/01/2023] [Revised: 03/29/2023] [Accepted: 05/03/2023] [Indexed: 05/30/2023]
Abstract
The contribution of mosaicism to diagnosed genetic disease and presumed de novo variants (DNV) is under investigated. We determined the contribution of mosaic genetic disease (MGD) and diagnosed parental mosaicism (PM) in parents of offspring with reported DNV (in the same variant) in the (1) Undiagnosed Diseases Network (UDN) (N = 1946) and (2) in 12,472 individuals electronic health records (EHR) who underwent genetic testing at an academic medical center. In the UDN, we found 4.51% of diagnosed probands had MGD, and 2.86% of parents of those with DNV exhibited PM. In the EHR, we found 6.03% and 2.99% and (of diagnosed probands) had MGD detected on chromosomal microarray and exome/genome sequencing, respectively. We found 2.34% (of those with a presumed pathogenic DNV) had a parent with PM for the variant. We detected mosaicism (regardless of pathogenicity) in 4.49% of genetic tests performed. We found a broad phenotypic spectrum of MGD with previously unknown phenotypic phenomena. MGD is highly heterogeneous and provides a significant contribution to genetic diseases. Further work is required to improve the diagnosis of MGD and investigate how PM contributes to DNV risk.
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Affiliation(s)
- Rory J Tinker
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kimberly Ezell
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Cecilia Esteves
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ellen F Macnamara
- Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rizwan Hamid
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Joy D Cogan
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - David Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Souhrid Mukharjee
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Ian Glass
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Katrina Dipple
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - John A Phillips
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Velazquez-Arcelay K, Colbran LL, McArthur E, Brand C, Rinker D, Siemann J, McMahon D, Capra JA. Archaic Introgression Shaped Human Circadian Traits. bioRxiv 2023:2023.02.03.527061. [PMID: 36778254 PMCID: PMC9915721 DOI: 10.1101/2023.02.03.527061] [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] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Introduction When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultra-violet radiation and increased variation in seasonal dynamics. However, whether these groups differed substantially in circadian biology, and whether archaic introgression adaptively contributed to human chronotypes remains unknown. Results Here we traced the evolution of chronotype based on genomes from archaic hominins and present-day humans. First, we inferred differences in circadian gene sequences, splicing, and regulation between archaic hominins and modern humans. We identified 28 circadian genes containing variants with potential to alter splicing in archaics (e.g., CLOCK, PER2, RORB, RORC), and 16 circadian genes likely divergently regulated between present-day humans and archaic hominins, including RORA. These differences suggest the potential for introgression to modify circadian gene expression. Testing this hypothesis, we found that introgressed variants are enriched among eQTLs for circadian genes. Supporting the functional relevance of these regulatory effects, we found that many introgressed alleles have associations with chronotype. Strikingly, the strongest introgressed effects on chronotype increase morningness, consistent with adaptations to high latitude in other species. Finally, we identified several circadian loci with evidence of adaptive introgression or latitudinal clines in allele frequency. Conclusions These findings identify differences in circadian gene regulation between modern humans and archaic hominins and support the contribution of introgression via coordinated effects on variation in human chronotype.
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Affiliation(s)
| | - Laura L. Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania
| | | | - Colin Brand
- Department of Epidemiology and Biostatistics, University of California, San Francisco
- Bakar Computational Health Sciences Institute, University of California, San Francisco
| | - David Rinker
- Department of Biological Sciences, Vanderbilt University
| | - Justin Siemann
- Department of Biological Sciences, Vanderbilt University
| | | | - John A. Capra
- Department of Epidemiology and Biostatistics, University of California, San Francisco
- Bakar Computational Health Sciences Institute, University of California, San Francisco
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Grunin M, de Jong S, Palmer EL, Jin B, Rinker D, Moth C, Capra A, Haines JL, Bush WS, den Hollander AI. Spatial Distribution of Missense Variants within Complement Proteins Associates with Age Related Macular Degeneration. medRxiv 2023:2023.08.28.23294686. [PMID: 37693462 PMCID: PMC10491280 DOI: 10.1101/2023.08.28.23294686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Purpose Genetic variants in complement genes are associated with age-related macular degeneration (AMD). However, many rare variants have been identified in these genes, but have an unknown significance, and their impact on protein function and structure is still unknown. We set out to address this issue by evaluating the spatial placement and impact on protein structureof these variants by developing an analytical pipeline and applying it to the International AMD Genomics Consortium (IAMDGC) dataset (16,144 AMD cases, 17,832 controls). Methods The IAMDGC dataset was imputed using the Haplotype Reference Consortium (HRC), leading to an improvement of over 30% more imputed variants, over the original 1000 Genomes imputation. Variants were extracted for the CFH , CFI , CFB , C9 , and C3 genes, and filtered for missense variants in solved protein structures. We evaluated these variants as to their placement in the three-dimensional structure of the protein (i.e. spatial proximity in the protein), as well as AMD association. We applied several pipelines to a) calculate spatial proximity to known AMD variants versus gnomAD variants, b) assess a variant's likelihood of causing protein destabilization via calculation of predicted free energy change (ddG) using Rosetta, and c) whole gene-based testing to test for statistical associations. Gene-based testing using seqMeta was performed using a) all variants b) variants near known AMD variants or c) with a ddG >|2|. Further, we applied a structural kernel adaptation of SKAT testing (POKEMON) to confirm the association of spatial distributions of missense variants to AMD. Finally, we used logistic regression on known AMD variants in CFI to identify variants leading to >50% reduction in protein expression from known AMD patient carriers of CFI variants compared to wild type (as determined by in vitro experiments) to determine the pipeline's robustness in identifying AMD-relevant variants. These results were compared to functional impact scores, ie CADD values > 10, which indicate if a variant may have a large functional impact genomewide, to determine if our metrics have better discriminative power than existing variant assessment methods. Once our pipeline had been validated, we then performed a priori selection of variants using this pipeline methodology, and tested AMD patient cell lines that carried those selected variants from the EUGENDA cohort (n=34). We investigated complement pathway protein expression in vitro , looking at multiple components of the complement factor pathway in patient carriers of bioinformatically identified variants. Results Multiple variants were found with a ddG>|2| in each complement gene investigated. Gene-based tests using known and novel missense variants identified significant associations of the C3 , C9 , CFB , and CFH genes with AMD risk after controlling for age and sex (P=3.22×10 -5 ;7.58×10 -6 ;2.1×10 -3 ;1.2×10 -31 ). ddG filtering and SKAT-O tests indicate that missense variants that are predicted to destabilize the protein, in both CFI and CFH, are associated with AMD (P=CFH:0.05, CFI:0.01, threshold of 0.05 significance). Our structural kernel approach identified spatial associations for AMD risk within the protein structures for C3, C9, CFB, CFH, and CFI at a nominal p-value of 0.05. Both ddG and CADD scores were predictive of reduced CFI protein expression, with ROC curve analyses indicating ddG is a better predictor (AUCs of 0.76 and 0.69, respectively). A priori in vitro analysis of variants in all complement factor genes indicated that several variants identified via bioinformatics programs PathProx/POKEMON in our pipeline via in vitro experiments caused significant change in complement protein expression (P=0.04) in actual patient carriers of those variants, via ELISA testing of proteins in the complement factor pathway, and were previously unknown to contribute to AMD pathogenesis. Conclusion We demonstrate for the first time that missense variants in complement genes cluster together spatially and are associated with AMD case/control status. Using this method, we can identify CFI and CFH variants of previously unknown significance that are predicted to destabilize the proteins. These variants, both in and outside spatial clusters, can predict in-vitro tested CFI protein expression changes, and we hypothesize the same is true for CFH . A priori identification of variants that impact gene expression allow for classification for previously classified as VUS. Further investigation is needed to validate the models for additional variants and to be applied to all AMD-associated genes.
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Steenwyk JL, Knowles S, Bastos RW, Balamurugan C, Rinker D, Mead ME, Roberts CD, Raja HA, Li Y, Colabardini AC, de Castro PA, dos Reis TF, Canóvas D, Sanchez RL, Lagrou K, Torrado E, Rodrigues F, Oberlies NH, Zhou X, Goldman GH, Rokas A. Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen. bioRxiv 2023:2023.07.03.547508. [PMID: 37461539 PMCID: PMC10350022 DOI: 10.1101/2023.07.03.547508] [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] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Cryptic fungal pathogens pose significant identification and disease management challenges due to their morphological resemblance to known pathogenic species while harboring genetic and (often) infectionrelevant trait differences. The cryptic fungal pathogen Aspergillus latus, an allodiploid hybrid originating from Aspergillus spinulosporus and an unknown close relative of Aspergillus quadrilineatus within section Nidulantes, remains poorly understood. The absence of accurate diagnostics for A. latus has led to misidentifications, hindering epidemiological studies and the design of effective treatment plans. We conducted an in-depth investigation of the genomes and phenotypes of 44 globally distributed isolates (41 clinical isolates and three type strains) from Aspergillus section Nidulantes. We found that 21 clinical isolates were A. latus; notably, standard methods of pathogen identification misidentified all A. latus isolates. The remaining isolates were identified as A. spinulosporus (8), A. quadrilineatus (1), or A. nidulans (11). Phylogenomic analyses shed light on the origin of A. latus, indicating one or two hybridization events gave rise to the species during the Miocene, approximately 15.4 to 8.8 million years ago. Characterizing the A. latus pangenome uncovered substantial genetic diversity within gene families and biosynthetic gene clusters. Transcriptomic analysis revealed that both parental genomes are actively expressed in nearly equal proportions and respond to environmental stimuli. Further investigation into infection-relevant chemical and physiological traits, including drug resistance profiles, growth under oxidative stress conditions, and secondary metabolite biosynthesis, highlight distinct phenotypic profiles of the hybrid A. latus compared to its parental and closely related species. Leveraging our comprehensive genomic and phenotypic analyses, we propose five genomic and phenotypic markers as diagnostics for A. latus species identification. These findings provide valuable insights into the evolutionary origin, genomic outcome, and phenotypic implications of hybridization in a cryptic fungal pathogen, thus enhancing our understanding of the underlying processes contributing to fungal pathogenesis. Furthermore, our study underscores the effectiveness of extensive genomic and phenotypic analyses as a promising approach for developing diagnostics applicable to future investigations of cryptic and emerging pathogens.
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Affiliation(s)
- Jacob L. Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Sonja Knowles
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Rafael W. Bastos
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
- Department of Microbiology and Parasitology, Bioscience Center, Federal University of Rio Grande do Norte, Natal-RN, Brazil
| | - Charu Balamurugan
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - David Rinker
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Matthew E. Mead
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Christopher D. Roberts
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Huzefa A. Raja
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Ana Cristina Colabardini
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Patrícia Alves de Castro
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Thaila Fernanda dos Reis
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - David Canóvas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Rafael Luperini Sanchez
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Department of Laboratory Medicine and National Reference Centre for Mycosis, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Egídio Torrado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4715-495 Braga, Portugal; ICVS/3B’s-PT Government Associate Laboratory, 4715-495 Braga, Portugal
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4715-495 Braga, Portugal; ICVS/3B’s-PT Government Associate Laboratory, 4715-495 Braga, Portugal
| | - Nicholas H. Oberlies
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Gustavo H. Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Antonis Rokas
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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Grunin M, Palmer E, de Jong S, Jin B, Rinker D, Moth C, Capra JA, Haines JL, Bush WS, den Hollander AI. Integrating Computational Approaches to Predict the Effect of Genetic Variants on Protein Stability in Retinal Degenerative Disease. Adv Exp Med Biol 2023; 1415:157-163. [PMID: 37440029 DOI: 10.1007/978-3-031-27681-1_24] [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] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Protein function can be impacted by changes in protein structure stability, but determining which change has impact is complex. Stability can be affected by a large change in the tertiary (3D) structure of the protein or due to free-energy changes caused by single amino acid substitutions. Changes in the DNA sequence can have minor or major impact on protein stability, which can lead to disease. Inherited retinal degenerations are generally caused by single mutations which are mostly located in protein-coding regions, while age-related macular degeneration (AMD) is a complex disorder that can be influenced by some genetic variants impacting proteins involved in the disease, although not all AMD risk variants lead to amino acid changes. Here, we review ways that proteins may be affected, the identification and understanding of these changes, and how to identify causal changes that can be targeted to develop treatments to alleviate retinal degenerative disease.
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Affiliation(s)
- Michelle Grunin
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.
| | - Ellen Palmer
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah de Jong
- Department of Ophthalmology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Bowen Jin
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - David Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Christopher Moth
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
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Kennedy T, Rinker D, Broadie K. Genetic background mutations drive neural circuit hyperconnectivity in a fragile X syndrome model. BMC Biol 2020; 18:94. [PMID: 32731855 PMCID: PMC7392683 DOI: 10.1186/s12915-020-00817-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/19/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Neural circuits are initially assembled during development when neurons synapse with potential partners and later refined as appropriate connections stabilize into mature synapses while inappropriate contacts are eliminated. Disruptions to this synaptogenic process impair connectivity optimization and can cause neurodevelopmental disorders. Intellectual disability (ID) and autism spectrum disorder (ASD) are often characterized by synaptic overgrowth, with the maintenance of immature or inappropriate synapses. Such synaptogenic defects can occur through mutation of a single gene, such as fragile X mental retardation protein (FMRP) loss causing the neurodevelopmental disorder fragile X syndrome (FXS). FXS represents the leading heritable cause of ID and ASD, but many other genes that play roles in ID and ASD have yet to be identified. RESULTS In a Drosophila FXS disease model, one dfmr150M null mutant stock exhibits previously unreported axonal overgrowths at developmental and mature stages in the giant fiber (GF) escape circuit. These excess axon projections contain both chemical and electrical synapse markers, indicating mixed synaptic connections. Extensive analyses show these supernumerary synapses connect known GF circuit neurons, rather than new, inappropriate partners, indicating hyperconnectivity within the circuit. Despite the striking similarities to well-characterized FXS synaptic defects, this new GF circuit hyperconnectivity phenotype is driven by genetic background mutations in this dfmr150M stock. Similar GF circuit synaptic overgrowth is not observed in independent dfmr1 null alleles. Bulked segregant analysis (BSA) was combined with whole genome sequencing (WGS) to identify the quantitative trait loci (QTL) linked to neural circuit hyperconnectivity. The results reveal 8 QTL associated with inappropriate synapse formation and maintenance in the dfmr150M mutant background. CONCLUSIONS Synaptogenesis is a complex, precisely orchestrated neurodevelopmental process with a large cohort of gene products coordinating the connectivity, synaptic strength, and excitatory/inhibitory balance between neuronal partners. This work identifies a number of genetic regions that contain mutations disrupting proper synaptogenesis within a particularly well-mapped neural circuit. These QTL regions contain potential new genes involved in synapse formation and refinement. Given the similarity of the synaptic overgrowth phenotype to known ID and ASD inherited conditions, identifying these genes should increase our understanding of these devastating neurodevelopmental disease states.
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Affiliation(s)
- Tyler Kennedy
- Department of Biological Sciences, Vanderbilt University and Medical Center, Nashville, TN, 37235, USA
| | - David Rinker
- Department of Biological Sciences, Vanderbilt University and Medical Center, Nashville, TN, 37235, USA
| | - Kendal Broadie
- Department of Biological Sciences, Vanderbilt University and Medical Center, Nashville, TN, 37235, USA.
- Department of Cell and Developmental Biology, Vanderbilt University and Medical Center, Nashville, TN, 37235, USA.
- Vanderbilt Brain Institute, Vanderbilt University and Medical Center, Nashville, TN, 37235, USA.
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Ackerman W, Buhimschi I, Eidem H, Rinker D, Rokas A, Rood K, Zhao G, Summerfield T, Landon M, Buhimschi C. 274: Next generation sequencing (RNA-seq) of the human decidual and placental villous transcriptomes in intra-amniotic infection (IAI) induced preterm birth (PTB). Am J Obstet Gynecol 2015. [DOI: 10.1016/j.ajog.2014.10.320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Castle A, Speranzini D, Rghei N, Alm G, Rinker D, Bissett J. Morphological and molecular identification of Trichoderma isolates on North American mushroom farms. Appl Environ Microbiol 1998; 64:133-7. [PMID: 9435070 PMCID: PMC124683 DOI: 10.1128/aem.64.1.133-137.1998] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/1996] [Accepted: 10/16/1997] [Indexed: 02/05/2023] Open
Abstract
Green mold disease (causal agent, Trichoderma) has resulted in severe crop losses on mushroom farms worldwide in recent years. We analyzed 160 isolates of Trichoderma from mushroom farms for morphological, cultural, and molecular characteristics and classified these isolates into phenotypic groups. The most common group comprised approximately 40% of the isolates and was identified as a strain of Trichoderma harzianum. This group was consistently recovered from farms with severe green mold disease but not from farms with little or no problem. In addition, the strain identified as the major cause of green mold disease in Ireland and the United Kingdom grouped with these North American isolates in having very similar randomly amplified polymorphic DNA patterns.
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Affiliation(s)
- A Castle
- Brock University, St. Catharines, Ontario, Canada.
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Affiliation(s)
- E Gut
- Abteilung Neuroradiologische Diagnostik/Kernspintomographie, Kliniken Schmieder, Neurologisches Fach- und Rehabilitationskrankenhaus, Allensbach
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