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Moussa DG, Sharma AK, Mansour TA, Witthuhn B, Perdigão J, Rudney JD, Aparicio C, Gomez A. Functional signatures of ex-vivo dental caries onset. J Oral Microbiol 2022; 14:2123624. [PMID: 36189437 PMCID: PMC9518263 DOI: 10.1080/20002297.2022.2123624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 05/16/2022] [Revised: 08/09/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
Background The etiology of dental caries remains poorly understood. With the advent of next-generation sequencing, a number of studies have focused on the microbial ecology of the disease. However, taxonomic associations with caries have not been consistent. Researchers have also pursued function-centric studies of the caries microbial communities aiming to identify consistently conserved functional pathways. A major question is whether changes in microbiome are a cause or a consequence of the disease. Thus, there is a critical need to define conserved functional signatures at the onset of dental caries. Methods Since it is unethical to induce carious lesions clinically, we developed an innovative longitudinal ex-vivo model integrated with the advanced non-invasive multiphoton second harmonic generation bioimaging to spot the very early signs of dental caries, combined with 16S rRNA short amplicon sequencing and liquid chromatography-mass spectrometry-based targeted metabolomics. Findings For the first time, we induced longitudinally monitored caries lesions validated with the scanning electron microscope. Consequently, we spotted the caries onset and, associated with it, distinguished five differentiating metabolites - Lactate, Pyruvate, Dihydroxyacetone phosphate, Glyceraldehyde 3-phosphate (upregulated) and Fumarate (downregulated). Those metabolites co-occurred with certain bacterial taxa; Streptococcus, Veillonella, Actinomyces, Porphyromonas, Fusobacterium, and Granulicatella, regardless of the abundance of other taxa. Interpretation These findings are crucial for understanding the etiology and dynamics of dental caries, and devising targeted interventions to prevent disease progression.
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Affiliation(s)
- Dina G. Moussa
- Minnesota Dental Research Center for Biomaterials and Biomechanics, Department of Restorative Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Animal Science, College of Food, Agriculture and Natural Resource Sciences, University of Minnesota, St Paul, Minnesota, USA
| | - Ashok K. Sharma
- Department of Animal Science, College of Food, Agriculture and Natural Resource Sciences, University of Minnesota, St Paul, Minnesota, USA
| | - Tamer A Mansour
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
- Department of Clinical Pathology, School of Medicine, Mansoura University, Mansoura, Egypt
| | - Bruce Witthuhn
- Center for Mass Spectrometry and Proteomics, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jorge Perdigão
- Department of Restorative Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Joel D. Rudney
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Conrado Aparicio
- Minnesota Dental Research Center for Biomaterials and Biomechanics, Department of Restorative Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Restorative Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andres Gomez
- Department of Animal Science, College of Food, Agriculture and Natural Resource Sciences, University of Minnesota, St Paul, Minnesota, USA
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Moussa DG, Ahmad P, Mansour TA, Siqueira WL. Current State and Challenges of the Global Outcomes of Dental Caries Research in the Meta-Omics Era. Front Cell Infect Microbiol 2022; 12:887907. [PMID: 35782115 PMCID: PMC9247192 DOI: 10.3389/fcimb.2022.887907] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/04/2022] [Indexed: 12/20/2022] Open
Abstract
Despite significant healthcare advances in the 21st century, the exact etiology of dental caries remains unsolved. The past two decades have witnessed a tremendous growth in our understanding of dental caries amid the advent of revolutionary omics technologies. Accordingly, a consensus has been reached that dental caries is a community-scale metabolic disorder, and its etiology is beyond a single causative organism. This conclusion was based on a variety of microbiome studies following the flow of information along the central dogma of biology from genomic data to the end products of metabolism. These studies were facilitated by the unprecedented growth of the next- generation sequencing tools and omics techniques, such as metagenomics and metatranscriptomics, to estimate the community composition of oral microbiome and its functional potential. Furthermore, the rapidly evolving proteomics and metabolomics platforms, including nuclear magnetic resonance spectroscopy and/or mass spectrometry coupled with chromatography, have enabled precise quantification of the translational outcomes. Although the majority supports ‘conserved functional changes’ as indicators of dysbiosis, it remains unclear how caries dynamics impact the microbiota functions and vice versa, over the course of disease onset and progression. What compounds the situation is the host-microbiota crosstalk. Genome-wide association studies have been undertaken to elucidate the interaction of host genetic variation with the microbiome. However, these studies are challenged by the complex interaction of host genetics and environmental factors. All these complementary approaches need to be orchestrated to capture the key players in this multifactorial disease. Herein, we critically review the milestones in caries research focusing on the state-of-art singular and integrative omics studies, supplemented with a bibliographic network analysis to address the oral microbiome, the host factors, and their interactions. Additionally, we highlight gaps in the dental literature and shed light on critical future research questions and study designs that could unravel the complexities of dental caries, the most globally widespread disease.
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Affiliation(s)
- Dina G. Moussa
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paras Ahmad
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Tamer A. Mansour
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States
- Department of Clinical Pathology, School of Medicine, Mansoura University, Mansoura, Egypt
| | - Walter L. Siqueira
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: Walter L. Siqueira,
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3
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Rolón‐Martínez S, Habib MR, Mansour TA, Díaz‐Ríos M, Rosenthal JJC, Zhou X, Croll RP, Miller MW. Cover Image, Volume 529, Issue 13. J Comp Neurol 2021. [DOI: 10.1002/cne.25214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Rolón-Martínez S, Habib MR, Mansour TA, Díaz-Ríos M, Rosenthal JJC, Zhou XN, Croll RP, Miller MW. FMRF-NH 2 -related neuropeptides in Biomphalaria spp., intermediate hosts for schistosomiasis: Precursor organization and immunohistochemical localization. J Comp Neurol 2021; 529:3336-3358. [PMID: 34041754 PMCID: PMC8273141 DOI: 10.1002/cne.25195] [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: 04/03/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 11/10/2022]
Abstract
Freshwater snails of the genus Biomphalaria serve as intermediate hosts for the digenetic trematode Schistosoma mansoni, the etiological agent for the most widespread form of intestinal schistosomiasis. As neuropeptide signaling in host snails can be altered by trematode infection, a neural transcriptomics approach was undertaken to identify peptide precursors in Biomphalaria glabrata, the major intermediate host for S. mansoni in the Western Hemisphere. Three transcripts that encode peptides belonging to the FMRF-NH2 -related peptide (FaRP) family were identified in B. glabrata. One transcript encoded a precursor polypeptide (Bgl-FaRP1; 292 amino acids) that included eight copies of the tetrapeptide FMRF-NH2 and single copies of FIRF-NH2 , FLRF-NH2 , and pQFYRI-NH2 . The second transcript encoded a precursor (Bgl-FaRP2; 347 amino acids) that comprised 14 copies of the heptapeptide GDPFLRF-NH2 and 1 copy of SKPYMRF-NH2 . The precursor encoded by the third transcript (Bgl-FaRP3; 287 amino acids) recapitulated Bgl-FaRP2 but lacked the full SKPYMRF-NH2 peptide. The three precursors shared a common signal peptide, suggesting a genomic organization described previously in gastropods. Immunohistochemical studies were performed on the nervous systems of B. glabrata and B. alexandrina, a major intermediate host for S. mansoni in Egypt. FMRF-NH2 -like immunoreactive (FMRF-NH2 -li) neurons were located in regions of the central nervous system associated with reproduction, feeding, and cardiorespiration. Antisera raised against non-FMRF-NH2 peptides present in the tetrapeptide and heptapeptide precursors labeled independent subsets of the FMRF-NH2 -li neurons. This study supports the participation of FMRF-NH2 -related neuropeptides in the regulation of vital physiological and behavioral systems that are altered by parasitism in Biomphalaria.
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Affiliation(s)
- Solymar Rolón-Martínez
- Institute of Neurobiology and Department of Anatomy and Neurobiology, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | - Mohamed R Habib
- Medical Malacology Laboratory, Theodor Bilharz Research Institute, Giza, Egypt
| | - Tamer A Mansour
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Clinical Pathology, School of Medicine, University of Mansoura, Mansoura, Egypt
| | | | | | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Roger P Croll
- Department of Physiology and Biophysics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Mark W Miller
- Institute of Neurobiology and Department of Anatomy and Neurobiology, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
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Shokrof M, Brown CT, Mansour TA. MQF and buffered MQF: quotient filters for efficient storage of k-mers with their counts and metadata. BMC Bioinformatics 2021; 22:71. [PMID: 33593271 PMCID: PMC7885209 DOI: 10.1186/s12859-021-03996-x] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/04/2021] [Indexed: 11/30/2022] Open
Abstract
Background Specialized data structures are required for online algorithms to efficiently handle large sequencing datasets. The counting quotient filter (CQF), a compact hashtable, can efficiently store k-mers with a skewed distribution.
Result Here, we present the mixed-counters quotient filter (MQF) as a new variant of the CQF with novel counting and labeling systems. The new counting system adapts to a wider range of data distributions for increased space efficiency and is faster than the CQF for insertions and queries in most of the tested scenarios. A buffered version of the MQF can offload storage to disk, trading speed of insertions and queries for a significant memory reduction. The labeling system provides a flexible framework for assigning labels to member items while maintaining good data locality and a concise memory representation. These labels serve as a minimal perfect hash function but are ~ tenfold faster than BBhash, with no need to re-analyze the original data for further insertions or deletions. Conclusions The MQF is a flexible and efficient data structure that extends our ability to work with high throughput sequencing data.
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Affiliation(s)
- Moustafa Shokrof
- Department of Computer Science, University of California, Davis, CA, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Tamer A Mansour
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA. .,Department of Clinical Pathology, School of Medicine, University of Mansoura, Mansoura, Egypt.
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6
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Owen JR, Hennig SL, McNabb BR, Mansour TA, Smith JM, Lin JC, Young AE, Trott JF, Murray JD, Delany ME, Ross PJ, Van Eenennaam AL. One-step generation of a targeted knock-in calf using the CRISPR-Cas9 system in bovine zygotes. BMC Genomics 2021; 22:118. [PMID: 33581720 PMCID: PMC7881600 DOI: 10.1186/s12864-021-07418-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/29/2020] [Accepted: 01/31/2021] [Indexed: 12/31/2022] Open
Abstract
Background The homologous recombination (HR) pathway is largely inactive in early embryos prior to the first cell division, making it difficult to achieve targeted gene knock-ins. The homology-mediated end joining (HMEJ)-based strategy has been shown to increase knock-in efficiency relative to HR, non-homologous end joining (NHEJ), and microhomology-mediated end joining (MMEJ) strategies in non-dividing cells. Results By introducing gRNA/Cas9 ribonucleoprotein complex and a HMEJ-based donor template with 1 kb homology arms flanked by the H11 safe harbor locus gRNA target site, knock-in rates of 40% of a 5.1 kb bovine sex-determining region Y (SRY)-green fluorescent protein (GFP) template were achieved in Bos taurus zygotes. Embryos that developed to the blastocyst stage were screened for GFP, and nine were transferred to recipient cows resulting in a live phenotypically normal bull calf. Genomic analyses revealed no wildtype sequence at the H11 target site, but rather a 26 bp insertion allele, and a complex 38 kb knock-in allele with seven copies of the SRY-GFP template and a single copy of the donor plasmid backbone. An additional minor 18 kb allele was detected that looks to be a derivative of the 38 kb allele resulting from the deletion of an inverted repeat of four copies of the SRY-GFP template. Conclusion The allelic heterogeneity in this biallelic knock-in calf appears to have resulted from a combination of homology directed repair, homology independent targeted insertion by blunt-end ligation, NHEJ, and rearrangement following editing of the gRNA target site in the donor template. This study illustrates the potential to produce targeted gene knock-in animals by direct cytoplasmic injection of bovine embryos with gRNA/Cas9, although further optimization is required to ensure a precise single-copy gene integration event. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07418-3.
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Affiliation(s)
- Joseph R Owen
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Sadie L Hennig
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Bret R McNabb
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Tamer A Mansour
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Department of Clinical Pathology, School of Medicine, University of Mansoura, Mansoura, Egypt
| | - Justin M Smith
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Jason C Lin
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Amy E Young
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Josephine F Trott
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - James D Murray
- Department of Animal Science, University of California - Davis, Davis, CA, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Mary E Delany
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Pablo J Ross
- Department of Animal Science, University of California - Davis, Davis, CA, USA
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7
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Vernau KM, Struys E, Letko A, Woolard KD, Aguilar M, Brown EA, Cissell DD, Dickinson PJ, Shelton GD, Broome MR, Gibson KM, Pearl PL, König F, Van Winkle TJ, O’Brien D, Roos B, Matiasek K, Jagannathan V, Drögemüller C, Mansour TA, Brown CT, Bannasch DL. A Missense Variant in ALDH5A1 Associated with Canine Succinic Semialdehyde Dehydrogenase Deficiency (SSADHD) in the Saluki Dog. Genes (Basel) 2020; 11:genes11091033. [PMID: 32887425 PMCID: PMC7565783 DOI: 10.3390/genes11091033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Dogs provide highly valuable models of human disease due to the similarity in phenotype presentation and the ease of genetic analysis. Seven Saluki puppies were investigated for neurological abnormalities including seizures and altered behavior. Magnetic resonance imaging showed a diffuse, marked reduction in cerebral cortical thickness, and symmetrical T2 hyperintensity in specific brain regions. Cerebral cortical atrophy with vacuolation (status spongiosus) was noted on necropsy. Genome-wide association study of 7 affected and 28 normal Salukis revealed a genome-wide significantly associated region on CFA 35. Whole-genome sequencing of three confirmed cases from three different litters revealed a homozygous missense variant within the aldehyde dehydrogenase 5 family member A1 (ALDH5A1) gene (XM_014110599.2: c.866G>A; XP_013966074.2: p.(Gly288Asp). ALDH5A1 encodes a succinic semialdehyde dehydrogenase (SSADH) enzyme critical in the gamma-aminobutyric acid neurotransmitter (GABA) metabolic pathway. Metabolic screening of affected dogs showed markedly elevated gamma-hydroxybutyric acid in serum, cerebrospinal fluid (CSF) and brain, and elevated succinate semialdehyde in urine, CSF and brain. SSADH activity in the brain of affected dogs was low. Affected Saluki dogs had striking similarities to SSADH deficiency in humans although hydroxybutyric aciduria was absent in affected dogs. ALDH5A1-related SSADH deficiency in Salukis provides a unique translational large animal model for the development of novel therapeutic strategies.
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Affiliation(s)
- Karen M. Vernau
- Department of Surgical and Radiological Sciences, University of California Davis, Davis, CA 95616, USA; (D.D.C.); (P.J.D.)
- Correspondence: (K.M.V.); (D.L.B.)
| | - Eduard Struys
- Department of Clinical Chemistry, VU University Medical Center, 1081 HV Amsterdam, The Netherlands; (E.S.); (B.R.)
| | - Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (A.L.); (V.J.); (C.D.)
| | - Kevin D. Woolard
- Department of Pathology, Microbiology and Immunology, University of California Davis, Davis, CA 95616, USA;
| | - Miriam Aguilar
- Department of Population Health and Reproduction, University of California Davis, Davis, CA 95616, USA; (M.A.); (E.A.B.); (T.A.M.); (C.T.B.)
| | - Emily A. Brown
- Department of Population Health and Reproduction, University of California Davis, Davis, CA 95616, USA; (M.A.); (E.A.B.); (T.A.M.); (C.T.B.)
| | - Derek D. Cissell
- Department of Surgical and Radiological Sciences, University of California Davis, Davis, CA 95616, USA; (D.D.C.); (P.J.D.)
| | - Peter J. Dickinson
- Department of Surgical and Radiological Sciences, University of California Davis, Davis, CA 95616, USA; (D.D.C.); (P.J.D.)
| | - G. Diane Shelton
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA;
| | | | - K. Michael Gibson
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA;
| | | | - Florian König
- Fachtierarzt fur Kleintiere, Am Berggewann 13, 65199 Wiesbaden, Germany;
| | - Thomas J. Van Winkle
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Dennis O’Brien
- College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA;
| | - B. Roos
- Department of Clinical Chemistry, VU University Medical Center, 1081 HV Amsterdam, The Netherlands; (E.S.); (B.R.)
| | - Kaspar Matiasek
- Clinical and Comparative Neuropathology, Ludwig-Maximilians-Universitaet München, 80539 Munchen, Germany;
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (A.L.); (V.J.); (C.D.)
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (A.L.); (V.J.); (C.D.)
| | - Tamer A. Mansour
- Department of Population Health and Reproduction, University of California Davis, Davis, CA 95616, USA; (M.A.); (E.A.B.); (T.A.M.); (C.T.B.)
- Department of Clinical Pathology, School of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - C. Titus Brown
- Department of Population Health and Reproduction, University of California Davis, Davis, CA 95616, USA; (M.A.); (E.A.B.); (T.A.M.); (C.T.B.)
| | - Danika L. Bannasch
- Department of Population Health and Reproduction, University of California Davis, Davis, CA 95616, USA; (M.A.); (E.A.B.); (T.A.M.); (C.T.B.)
- Correspondence: (K.M.V.); (D.L.B.)
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Mansour TA, Woolard KD, Vernau KL, Ancona DM, Thomasy SM, Sebbag L, Moore BA, Knipe MF, Seada HA, Cowan TM, Aguilar M, Titus Brown C, Bannasch DL. Whole genome sequencing for mutation discovery in a single case of lysosomal storage disease (MPS type 1) in the dog. Sci Rep 2020; 10:6558. [PMID: 32300136 PMCID: PMC7162951 DOI: 10.1038/s41598-020-63451-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/06/2020] [Indexed: 01/08/2023] Open
Abstract
Mucopolysaccharidosis (MPS) is a metabolic storage disorder caused by the deficiency of any lysosomal enzyme required for the breakdown of glycosaminoglycans. A 15-month-old Boston Terrier presented with clinical signs consistent with lysosomal storage disease including corneal opacities, multifocal central nervous system disease and progressively worsening clinical course. Diagnosis was confirmed at necropsy based on histopathologic evaluation of multiple organs demonstrating accumulation of mucopolysaccharides. Whole genome sequencing was used to uncover a frame-shift insertion affecting the alpha-L-iduronidase (IDUA) gene (c.19_20insCGGCCCCC), a mutation confirmed in another Boston Terrier presented 2 years later with a similar clinical picture. Both dogs were homozygous for the IDUA mutation and shared coat colors not recognized as normal for the breed by the American Kennel Club. In contrast, the mutation was not detected in 120 unrelated Boston Terriers as well as 202 dogs from other breeds. Recent inbreeding to select for recessive and unusual coat colors may have concentrated this relatively rare allele in the breed. The identification of the variant enables ante-mortem diagnosis of similar cases and selective breeding to avoid the spread of this disease in the breed. Boston Terriers carrying this variant represent a promising model for MPS I with neurological abnormalities in humans.
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Affiliation(s)
- Tamer A Mansour
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States.
- Department of Clinical Pathology, School of Medicine, Mansoura University, Mansoura, Egypt.
| | - Kevin D Woolard
- Department of Pathology, Immunology and Microbiology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Karen L Vernau
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Devin M Ancona
- VCA West Coast Specialty and Emergency Animal Hospital, Fountain Valley, CA, United States
| | - Sara M Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, CA, United States
- Department of Ophthalmology & Vision Science, School of Medicine, University of California, Davis, CA, United States
| | - Lionel Sebbag
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Bret A Moore
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Marguerite F Knipe
- William R Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Haitham A Seada
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Tina M Cowan
- Department of Pathology, Stanford University, Palo Alto, CA, United States
| | - Miriam Aguilar
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - C Titus Brown
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Danika L Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States.
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9
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Kousa YA, Zhu H, Fakhouri WD, Lei Y, Kinoshita A, Roushangar RR, Patel NK, Agopian AJ, Yang W, Leslie EJ, Busch TD, Mansour TA, Li X, Smith AL, Li EB, Sharma DB, Williams TJ, Chai Y, Amendt BA, Liao EC, Mitchell LE, Bassuk AG, Gregory S, Ashley-Koch A, Shaw GM, Finnell RH, Schutte BC. The TFAP2A-IRF6-GRHL3 genetic pathway is conserved in neurulation. Hum Mol Genet 2020; 28:1726-1737. [PMID: 30689861 DOI: 10.1093/hmg/ddz010] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 11/26/2018] [Accepted: 12/31/2018] [Indexed: 02/06/2023] Open
Abstract
Mutations in IRF6, TFAP2A and GRHL3 cause orofacial clefting syndromes in humans. However, Tfap2a and Grhl3 are also required for neurulation in mice. Here, we found that homeostasis of Irf6 is also required for development of the neural tube and associated structures. Over-expression of Irf6 caused exencephaly, a rostral neural tube defect, through suppression of Tfap2a and Grhl3 expression. Conversely, loss of Irf6 function caused a curly tail and coincided with a reduction of Tfap2a and Grhl3 expression in tail tissues. To test whether Irf6 function in neurulation was conserved, we sequenced samples obtained from human cases of spina bifida and anencephaly. We found two likely disease-causing variants in two samples from patients with spina bifida. Overall, these data suggest that the Tfap2a-Irf6-Grhl3 genetic pathway is shared by two embryologically distinct morphogenetic events that previously were considered independent during mammalian development. In addition, these data suggest new candidates to delineate the genetic architecture of neural tube defects and new therapeutic targets to prevent this common birth defect.
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Affiliation(s)
- Youssef A Kousa
- Departments of Biochemistry and Molecular Biology.,Division of Neurology, Childrens National Health System.,Center for Neuroscience Research, The Childrens Research Institute, Washington, DC, USA
| | - Huiping Zhu
- Dell Pediatric Research Institute, Department of Nutritional Sciences, University of Texas at Austin, Austin, TX, USA
| | - Walid D Fakhouri
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yunping Lei
- Dell Pediatric Research Institute, Department of Nutritional Sciences, University of Texas at Austin, Austin, TX, USA
| | - Akira Kinoshita
- Department of Human Genetics, Nagasaki University, Nagasaki, Japan
| | | | | | - A J Agopian
- Human Genetics Center, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
| | - Wei Yang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Tamer A Mansour
- Genetics PhD Program.,Department of Clinical Pathology, School of Medicine, University of Mansoura, Mansoura, Egypt.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Xiao Li
- Anatomy and Cell Biology, University of Iowa, Iowa City, IA, USA
| | | | - Edward B Li
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Dhruv B Sharma
- Center for Statistical Training & Consulting, Michigan State University, East Lansing, MI, USA
| | - Trevor J Williams
- Department of Craniofacial Biology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Brad A Amendt
- Anatomy and Cell Biology, University of Iowa, Iowa City, IA, USA
| | - Eric C Liao
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Laura E Mitchell
- Human Genetics Center, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
| | | | - Simon Gregory
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Allison Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard H Finnell
- Dell Pediatric Research Institute, Department of Nutritional Sciences, University of Texas at Austin, Austin, TX, USA
| | - Brian C Schutte
- Departments of Biochemistry and Molecular Biology.,Microbiology and Molecular Genetics.,Genetics PhD Program.,Pediatrics and Human Development
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10
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Young AE, Mansour TA, McNabb BR, Owen JR, Trott JF, Brown CT, Van Eenennaam AL. Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull. Nat Biotechnol 2020; 38:225-232. [PMID: 31591551 PMCID: PMC7007412 DOI: 10.1038/s41587-019-0266-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [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: 02/04/2019] [Accepted: 08/28/2019] [Indexed: 12/20/2022]
Abstract
Genome editing followed by reproductive cloning was previously used to produce two hornless dairy bulls. We crossed one genome-edited dairy bull, homozygous for the dominant PC Celtic POLLED allele, with horned cows (pp) and obtained six heterozygous (PCp) polled calves. The calves had no horns and were otherwise healthy and phenotypically unremarkable. We conducted whole-genome sequencing of all animals using an Illumina HiSeq4000 to achieve ~20× coverage. Bioinformatics analyses revealed the bull was a compound heterozygote, carrying one naturally occurring PC Celtic POLLED allele and an allele containing an additional introgression of the homology-directed repair donor plasmid along with the PC Celtic allele. These alleles segregated in the offspring of this bull, and inheritance of either allele produced polled calves. No other unintended genomic alterations were observed. These data can be used to inform conversations in the scientific community, with regulatory authorities and with the public around 'intentional genomic alterations' and future regulatory actions regarding genome-edited animals.
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Affiliation(s)
- Amy E Young
- Department of Animal Science, University of California, Davis, CA, USA
| | - Tamer A Mansour
- Department of Clinical Pathology, School of Medicine, University of Mansoura, Mansoura, Egypt
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Bret R McNabb
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Joseph R Owen
- Department of Animal Science, University of California, Davis, CA, USA
| | - Josephine F Trott
- Department of Animal Science, University of California, Davis, CA, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
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11
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Young AE, Mansour TA, McNabb BR, Owen JR, Trott JF, Brown CT, Van Eenennaam AL. Author Correction: Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull. Nat Biotechnol 2020; 38:245. [PMID: 31992864 PMCID: PMC7007411 DOI: 10.1038/s41587-020-0423-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amy E Young
- Department of Animal Science, University of California, Davis, CA, USA
| | - Tamer A Mansour
- Department of Clinical Pathology, School of Medicine, University of Mansoura, Mansoura, Egypt.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Bret R McNabb
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Joseph R Owen
- Department of Animal Science, University of California, Davis, CA, USA
| | - Josephine F Trott
- Department of Animal Science, University of California, Davis, CA, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
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12
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Mansour TA, Rosenthal JJC, Brown CT, Roberson LM. Correction to: Transcriptome of the caribbean stony coral Porites astreoides from three developmental stages. Gigascience 2019; 8:5626376. [PMID: 31730696 PMCID: PMC6857687 DOI: 10.1093/gigascience/giz048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Tamer A Mansour
- Department of Population Health and Reproduction, University of California, Davis, California, USA.,Department of Clinical Pathology, College of Medicine, Mansoura University, Mansoura, Egypt
| | - Joshua J C Rosenthal
- Marine Biological Laboratory, Woods Hole, Massachusetts, USA.,Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, University of California, Davis, California, USA
| | - Loretta M Roberson
- Marine Biological Laboratory, Woods Hole, Massachusetts, USA.,Department of Environmental Science, University of Puerto Rico Río Piedras, San Juan, Puerto Rico, USA
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13
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Mansour TA, Lucot K, Konopelski SE, Dickinson PJ, Sturges BK, Vernau KL, Choi S, Stern JA, Thomasy SM, Döring S, Verstraete FJM, Johnson EG, York D, Rebhun RB, Ho HYH, Brown CT, Bannasch DL. Whole genome variant association across 100 dogs identifies a frame shift mutation in DISHEVELLED 2 which contributes to Robinow-like syndrome in Bulldogs and related screw tail dog breeds. PLoS Genet 2018; 14:e1007850. [PMID: 30521570 PMCID: PMC6303079 DOI: 10.1371/journal.pgen.1007850] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/21/2018] [Accepted: 11/24/2018] [Indexed: 12/30/2022] Open
Abstract
Domestic dog breeds exhibit remarkable morphological variations that result from centuries of artificial selection and breeding. Identifying the genetic changes that contribute to these variations could provide critical insights into the molecular basis of tissue and organismal morphogenesis. Bulldogs, French Bulldogs and Boston Terriers share many morphological and disease-predisposition traits, including brachycephalic skull morphology, widely set eyes and short stature. Unlike other brachycephalic dogs, these breeds also exhibit vertebral malformations that result in a truncated, kinked tail (screw tail). Whole genome sequencing of 100 dogs from 21 breeds identified 12.4 million bi-allelic variants that met inclusion criteria. Whole Genome Association of these variants with the breed defining phenotype of screw tail was performed using 10 cases and 84 controls and identified a frameshift mutation in the WNT pathway gene DISHEVELLED 2 (DVL2) (Chr5: 32195043_32195044del, p = 4.37 X 10-37) as the most strongly associated variant in the canine genome. This DVL2 variant was fixed in Bulldogs and French Bulldogs and had a high allele frequency (0.94) in Boston Terriers. The DVL2 variant segregated with thoracic and caudal vertebral column malformations in a recessive manner with incomplete and variable penetrance for thoracic vertebral malformations between different breeds. Importantly, analogous frameshift mutations in the human DVL1 and DVL3 genes cause Robinow syndrome, a congenital disorder characterized by similar craniofacial, limb and vertebral malformations. Analysis of the canine DVL2 variant protein showed that its ability to undergo WNT-induced phosphorylation is reduced, suggesting that altered WNT signaling may contribute to the Robinow-like syndrome in the screwtail breeds.
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Affiliation(s)
- Tamer A. Mansour
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America
- Department of Clinical Pathology, School of Medicine, University of Mansoura, Mansoura Egypt
| | - Katherine Lucot
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America
- Integrative Genetics and Genomics Graduate Group, University of California Davis, Davis, CA, United States of America
| | - Sara E. Konopelski
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California Davis, Davis, CA, United States of America
| | - Peter J. Dickinson
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America
| | - Beverly K. Sturges
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America
| | - Karen L. Vernau
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America
| | - Shannon Choi
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California Davis, Davis, CA, United States of America
| | - Joshua A. Stern
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America
| | - Sara M. Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America
| | - Sophie Döring
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America
| | - Frank J. M. Verstraete
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America
| | - Eric G. Johnson
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America
| | - Daniel York
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America
| | - Robert B. Rebhun
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America
| | - Hsin-Yi Henry Ho
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California Davis, Davis, CA, United States of America
| | - C. Titus Brown
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America
- Genome Center, University of California Davis, Davis, CA, United States of America
| | - Danika L. Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America
- Genome Center, University of California Davis, Davis, CA, United States of America
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14
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Mansour TA, Habib MR, Rodríguez LCV, Vázquez AH, Alers JM, Ghezzi A, Croll RP, Brown CT, Miller MW. Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis. BMC Res Notes 2017; 10:729. [PMID: 29228974 PMCID: PMC5725652 DOI: 10.1186/s13104-017-3018-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/31/2017] [Indexed: 11/26/2022] Open
Abstract
Objective Globally, more than 200 million people live at risk of the neglected tropical disease schistosomiasis (or snail fever). Larval schistosomes require the presence of specific snail species that act as intermediate hosts, supporting their multiplication and transformation into forms that can infect humans. This project was designed to generate a transcriptome from the central nervous system (CNS) of Biomphalaria alexandrina, the major intermediate host for Schistosoma mansoni in Egypt. Results A transcriptome was generated from five pooled central nervous systems dissected from uninfected specimens of B. alexandrina. Raw Illumina RNA-seq data (~ 20.3 million paired end reads of 150 base pairs length each) generated a transcriptome consisting of 144,213 transcript elements with an N50 contig size of 716 base pairs. Orthologs of 15,246 transcripts and homologs for an additional 16,810 transcripts were identified in the UniProtKB/Swiss-Prot database. The B. alexandrina CNS transcriptome provides a resource for future research exploring parasite-host interactions in a simpler nervous system. Moreover, increased understanding of the neural signaling mechanisms involved in the response of B. alexandrina to infection by S. mansoni larvae could lead to novel and highly specific strategies for the control of snail populations. Electronic supplementary material The online version of this article (10.1186/s13104-017-3018-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tamer A Mansour
- Department of Population Health and Reproduction, University of California, Davis, CA, USA.,Department of Clinical Pathology, College of Medicine, Mansoura University, Mansoura, Egypt
| | - Mohamed R Habib
- Medical Malacology Department, Theodor Bilharz Research Institute, Giza, 12411, Egypt
| | - Laura C Vicente Rodríguez
- Institute of Neurobiology and Department of Anatomy & Neurobiology, University of Puerto Rico, Medical Sciences Campus, 201 Blvd del Valle, San Juan, Puerto Rico
| | - Anthony Hernández Vázquez
- Institute of Neurobiology and Department of Anatomy & Neurobiology, University of Puerto Rico, Medical Sciences Campus, 201 Blvd del Valle, San Juan, Puerto Rico
| | - Julián Maldonado Alers
- Institute of Neurobiology and Department of Anatomy & Neurobiology, University of Puerto Rico, Medical Sciences Campus, 201 Blvd del Valle, San Juan, Puerto Rico
| | - Alfredo Ghezzi
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico
| | - Roger P Croll
- Department of Physiology and Biophysics, Dalhousie University, Halifax, NS, Canada
| | - C Titus Brown
- Department of Population Health and Reproduction, University of California, Davis, CA, USA
| | - Mark W Miller
- Institute of Neurobiology and Department of Anatomy & Neurobiology, University of Puerto Rico, Medical Sciences Campus, 201 Blvd del Valle, San Juan, Puerto Rico.
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15
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Kousa YA, Mansour TA, Seada H, Matoo S, Schutte BC. Shared molecular networks in orofacial and neural tube development. Birth Defects Res 2017; 109:169-179. [DOI: 10.1002/bdra.23598] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 10/17/2016] [Accepted: 10/21/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Youssef A. Kousa
- Pediatric Residency Program; Children's National Health System; Washington DC
| | - Tamer A. Mansour
- Department of Population Health and Reproduction; University of California; Davis California
- Department of Clinical Pathology, College of Medicine; Mansoura University; Egypt
| | - Haitham Seada
- Department of Computer Science and Engineering, Computational Optimization and Innovation Laboratory; Michigan State University; East Lansing Michigan
| | - Samaneh Matoo
- Department of Modern Science; Islamic Azad University-Tehran Medical Branch; Tehran Iran
| | - Brian C. Schutte
- Department of Microbiology and Molecular Genetics and the Department of Pediatrics and Human Development; Michigan State University; East Lansing Michigan
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16
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Mansour TA, Scott EY, Finno CJ, Bellone RR, Mienaltowski MJ, Penedo MC, Ross PJ, Valberg SJ, Murray JD, Brown CT. Tissue resolved, gene structure refined equine transcriptome. BMC Genomics 2017; 18:103. [PMID: 28107812 PMCID: PMC5251313 DOI: 10.1186/s12864-016-3451-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 09/24/2016] [Accepted: 12/21/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome. RESULTS This equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution, while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome. CONCLUSIONS We have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and are flexible for several downstream analyses. We encourage the integration of further equine transcriptomes with our annotation pipeline to continue and improve the equine transcriptome.
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Affiliation(s)
- T A Mansour
- Department of Population Health and Reproduction, University of California, Davis, Davis, USA.,Department of Clinical Pathology, College of Medicine, Mansoura University, Egypt, Mansoura, Egypt
| | - E Y Scott
- Department of Animal Science, University of California, Davis, Davis, USA
| | - C J Finno
- Department of Population Health and Reproduction, University of California, Davis, Davis, USA
| | - R R Bellone
- Department of Population Health and Reproduction, University of California, Davis, Davis, USA.,Veterinary Genetics Laboratory, University of California, Davis, Davis, USA
| | - M J Mienaltowski
- Department of Animal Science, University of California, Davis, Davis, USA
| | - M C Penedo
- Veterinary Genetics Laboratory, University of California, Davis, Davis, USA
| | - P J Ross
- Department of Animal Science, University of California, Davis, Davis, USA
| | - S J Valberg
- Large Animal Clinical Sciences, Michigan State University, College of Veterinary Medicine, East Lansing, USA
| | - J D Murray
- Department of Population Health and Reproduction, University of California, Davis, Davis, USA.,Department of Animal Science, University of California, Davis, Davis, USA
| | - C T Brown
- Department of Population Health and Reproduction, University of California, Davis, Davis, USA.
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17
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Mansour TA, Rosenthal JJC, Brown CT, Roberson LM. Transcriptome of the Caribbean stony coral Porites astreoides from three developmental stages. Gigascience 2016; 5:33. [PMID: 27485233 PMCID: PMC4969664 DOI: 10.1186/s13742-016-0138-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 02/19/2016] [Accepted: 07/14/2016] [Indexed: 11/24/2022] Open
Abstract
Background Porites astreoides is a ubiquitous species of coral on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most other coral species. We assembled and annotated a transcriptome from this coral using Illumina sequences from three different developmental stages collected over several years: free-swimming larvae, newly settled larvae, and adults (>10 cm in diameter). This resource will aid understanding of coral calcification, larval settlement, and host–symbiont interactions. Findings A de novo transcriptome for the P. astreoides holobiont (coral plus algal symbiont) was assembled using 594 Mbp of raw Illumina sequencing data generated from five age-specific cDNA libraries. The new transcriptome consists of 867 255 transcript elements with an average length of 685 bases. The isolated P. astreoides assembly consists of 129 718 transcript elements with an average length of 811 bases, and the isolated Symbiodinium sp. assembly had 186 177 transcript elements with an average length of 1105 bases. Conclusions This contribution to coral transcriptome data provides a valuable resource for researchers studying the ontogeny of gene expression patterns within both the coral and its dinoflagellate symbiont.
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Affiliation(s)
- Tamer A Mansour
- Department of Population Health and Reproduction, University of California, Davis, California, USA.,Department of Clinical Pathology, College of Medicine, Mansoura University, Mansoura, Egypt
| | - Joshua J C Rosenthal
- Marine Biological Laboratory, Woods Hole, Massachusetts, USA.,Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, University of California, Davis, California, USA
| | - Loretta M Roberson
- Marine Biological Laboratory, Woods Hole, Massachusetts, USA. .,Department of Environmental Science, University of Puerto Rico Río Piedras, San Juan, Puerto Rico, USA.
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18
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de la Garza G, Schleiffarth JR, Dunnwald M, Mankad A, Weirather JL, Bonde G, Butcher S, Mansour TA, Kousa YA, Fukazawa CF, Houston DW, Manak JR, Schutte BC, Wagner DS, Cornell RA. Interferon regulatory factor 6 promotes differentiation of the periderm by activating expression of Grainyhead-like 3. J Invest Dermatol 2012; 133:68-77. [PMID: 22931925 PMCID: PMC3541433 DOI: 10.1038/jid.2012.269] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Interferon Regulatory Factor 6 (IRF6) is a transcription factor that, in mammals, is required for the differentiation of skin, breast epithelium, and oral epithelium. However, the transcriptional targets that mediate these effects are currently unknown. In zebrafish and frog embryos Irf6 is necessary for differentiation of the embryonic superficial epithelium, or periderm. Here we use microarrays to identify genes that are expressed in the zebrafish periderm and whose expression is inhibited by a dominant-negative variant of Irf6 (dnIrf6). These methods identify Grhl3, an ancient regulator of the epidermal permeability barrier, as acting downstream of Irf6. In human keratinocytes, IRF6 binds conserved elements near the GHRL3 promoter. We show that one of these elements has enhancer activity in human keratinocytes and zebrafish periderm, suggesting that Irf6 directly stimulates Grhl3 expression in these tissues. Simultaneous inhibition of grhl1 and grhl3 disrupts periderm differentiation in zebrafish, and, intriguingly, forced grhl3 expression restores periderm markers in both zebrafish injected with dnIrf6 and frog embryos depleted of Irf6. Finally, in Irf6 deficient mouse embryos, Grhl3 expression in the periderm and oral epithelium is virtually absent. These results indicate that Grhl3 is a key effector of Irf6 in periderm differentiation.
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Affiliation(s)
- Gabriel de la Garza
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa, Iowa City, IA, USA
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19
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Noweir MB, Osman HA, Abbas FI, Abou-Taleb AM, Mansour TA. Child labour in Egypt. II. Impact of work environment on health. J Egypt Public Health Assoc 1993; 68:443-67. [PMID: 17265656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The studied population (1000 children and young workers and 250 controls) were interviewed for health complaints and subjected to extensive medical investigations. Health problems are more encountered among the workers than in the controls, which has been attributed to the impact of work on health and to the low socioeconomic background that compels the children to work, which may constitute a potential health problem from the start. The significant health problems include: a) Respiratory system complaints, attacks of cough, chronic bronchitis, bronchial asthma and reduction in FEV1.0/FVC; b) cardiovascular abnormalities including palpitations, sinus tachycardia, anemia, vertigo and syncope; c) gastrointestinal abnormalities including dyspepsia and parasitic infestations; d) neuropsychiatric complaints; and e) other health problems including urinary tract infections, backache, visual impairment, repair of hernia and nocturnal enuresis. The study has been concluded by recommending the use of primary health care approach to child labour, emphasizing the importance of pre-employment and periodical medical examinations for protecting this vulnerable group from work hazards, and expanding the efforts of family planning to reduce family size.
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Affiliation(s)
- M B Noweir
- Occupational Health Department, High Institute of Public Health, Alexandria University, Egypt
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20
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Noweir MH, Oman HA, Abbas FI, Abou-Taleb AM, Mansour TA. Child labour in Egypt. I. Occupational and socio-economic aspects. J Egypt Public Health Assoc 1993; 68:405-42. [PMID: 17265655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The present study comprised 1000 child and young workers in small and medium-size industries in Alexandria, as well as 250 control subjects. Almost all young workers work for more than 40 hours/week and suffer from fatigue. Workers' family needs rather than the lack of family care is the responsible factor for sending the child to work, and the economic problems seem to be the underlying factor for all other problems of child labour. Work improves labourers' socio-economic status and smoking habit, and provides a chance for their personal contacts and interactions, which are reflected on their level of intellectual capabilities; however, it has some impact on their food habits affecting their achievement of balanced diet; and no drug addiction exists among all the studied subjects. Noise and dust represent the main occupational exposures (84.4% and 55.8% respectively), followed by exposure to heat (25.3%), vapors and gases (10.4%) and biological materials (9.0%), and nearly 2/3 of the workers have combined exposures. Work injuries occurred to 18.4% of the workers and 7.4% had more than one injury during employment; however, nearly 1/3 of the injuries required absenteeism off work and/or hospitalization. The injuries have been typically related to industrial operations, occurring mostly to hands and fingers (80.4%), and are mainly attributed to lack of training (63.0%). The health services presented to the workers are very poor. The study has been concluded by recommending making the work safe, free from hazards, and ergonomically fit to children, providing educational and training services, covering young workers by social security, and revising legislation of child labour.
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Affiliation(s)
- M H Noweir
- Occupational Health Department, High Institute of Public Health, Alexandria University, Egypt
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