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Khan NF, Ahmed SS, Abdulraheem MI, Reshi ZA, Wahab A, Abdi G. Deciphering mycobiota and its functional dynamics in root hairs of Rhododendron campanulatum D. Don through Next-gen sequencing. Sci Rep 2024; 14:10294. [PMID: 38704448 PMCID: PMC11069570 DOI: 10.1038/s41598-024-61120-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 05/02/2024] [Indexed: 05/06/2024] Open
Abstract
The Himalayas provide unique opportunities for the extension of shrubs beyond the upper limit of the tree. However, little is known about the limitation of the biotic factors belowground of shrub growth at these cruising altitudes. To fill this gap, the present study deals with the documentation of root-associated microbiota with their predicted functional profiles and interactions in the host Rhododendron campanulatum, a krummholz species. While processing 12 root samples of R. campanulatum from the sites using Omics we could identify 134 root-associated fungal species belonging to 104 genera, 74 families, 39 orders, 17 classes, and 5 phyla. The root-associated microbiota members of Ascomycota were unambiguously dominant followed by Basidiomycota. Using FUNGuild, we reported that symbiotroph and pathotroph as abundant trophic modes. Furthermore, FUNGuild revealed the dominant prevalence of the saptroptroph guild followed by plant pathogens and wood saprotrophs. Alpha diversity was significantly different at the sites. The heatmap dendrogram showed the correlation between various soil nutrients and some fungal species. The study paves the way for a more in-depth exploration of unidentified root fungal symbionts, their interactions and their probable functional roles, which may serve as an important factor for the growth and conservation of these high-altitude ericaceous plants.
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Affiliation(s)
- Nafeesa Farooq Khan
- Biological Invasion Lab, Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190006, India.
| | - Sheikh Sajad Ahmed
- Biological Invasion Lab, Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190006, India
| | - Mukhtar Iderawumi Abdulraheem
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou, 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou, 450002, China
| | - Zafar Ahmad Reshi
- Biological Invasion Lab, Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190006, India
| | - Abdul Wahab
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Center for Plant Stress Biology, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Gholamreza Abdi
- Department of Biotechnology, Persian Gul Research Institute, Persian Gulf University, Bushehr, 75169, Iran.
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Walkley SU, Molholm S, Jordan B, Marion RW, Wasserstein M. Using team-based precision medicine to advance understanding of rare genetic brain disorders. J Neurodev Disord 2024; 16:10. [PMID: 38491427 PMCID: PMC10941544 DOI: 10.1186/s11689-024-09518-z] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/07/2024] [Indexed: 03/18/2024] Open
Abstract
We describe a multidisciplinary teamwork approach known as "Operation IDD Gene Team" developed by the Rose F. Kennedy Intellectual and Developmental Disabilities Research Center (RFK IDDRC) at the Albert Einstein College of Medicine. This initiative brings families affected by rare genetic diseases that cause intellectual and developmental disability together with physicians, basic scientists, and their trainees. At team meetings, family members share their child's medical and personal history, physicians describe the broader clinical consequences of the condition, and scientists provide accessible tutorials focused on the fundamental biology of relevant genes. When appropriate, possible treatment approaches are also discussed. The outcomes of team meetings have been overwhelmingly positive, with families not only expressing deep gratitude, but also becoming empowered to establish foundations dedicated to their child's specific condition. Physicians, and in particular the scientists and their trainees, have gained a deeper understanding of challenges faced by affected families, broadening their perspective on how their research can extend beyond the laboratory. Remarkably, research by the scientists following the Gene Team meetings have often included focus on the actual gene variants exhibited by the participating children. As these investigations progress and newly created foundations expand their efforts, national as well as international collaborations are forged. These developments emphasize the importance of rare diseases as windows into previously unexplored molecular and cellular processes, which can offer fresh insights into both normal function as well as more common diseases. Elucidating the mechanisms of and treatments for rare and ultra-rare diseases thus has benefits for all involved-families, physicians, and scientists and their trainees, as well as the broader medical community. While the RFK IDDRC's Operation IDD Gene Team program has focused on intellectual disabilities affecting children, we believe it has the potential to be applied to rare genetic diseases impacting individuals of any age and encompassing a wide variety of developmental disorders affecting multiple organ systems.
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Affiliation(s)
- Steven U Walkley
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Department of Neuroscience, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Sophie Molholm
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Bryen Jordan
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Robert W Marion
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Melissa Wasserstein
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
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Chan KWK, Bifani AM, Watanabe S, Choy MM, Ooi EE, Vasudevan SG. Tissue-specific expansion of Zika virus isogenic variants drive disease pathogenesis. EBioMedicine 2023; 91:104570. [PMID: 37068347 PMCID: PMC10130475 DOI: 10.1016/j.ebiom.2023.104570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/09/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND The Asian lineage Zika virus (ZIKV) emerged as a public health emergency in 2016 causing severe neurological pathologies with no apparent historical correlate to the mild, disease-causing innocuous member of the mosquito-borne flavivirus genus that was discovered in Africa in 1947. Replication error rate of RNA viruses combined with viral protein/RNA structural plasticity can lead to evolution of virus-induced pathogenicity that is critical to identify and validate. METHODS Infection studies in cells and A129 interferon alpha/beta receptor deficient mice with ZIKV French Polynesian H/PF/2013 clinical isolate, plaque-purified isogenic clone derivatives as well as infectious cDNA clone derived wild-type and site-specific mutant viruses, were employed together with Next-Generation Sequencing (NGS) to pin-point the contributions of specific viral variants in neurovirulence recapitulated in our ZIKV mouse model. FINDINGS NGS analysis of the low-passage inoculum virus as well as mouse serum, brain and testis derived virus, revealed specific enrichment in the mouse brain that were not found in the other tissues. Specifically, non-structural (NS) protein 2A variant at position 117 along with changes in NS1 and NS4B were uniquely associated with the mouse brain isolate. Mutational analysis of these variants in cDNA infectious clones identified the NS2A A117V as the lethal pathogenic determinant with potential epistatic contribution of NS1 and NS4B variants in ZIKV brain penetrance. INTERPRETATION Our findings confirm that viral subpopulations drive ZIKV neuropathogenicity and identify specific sequence variants that expand in the mouse brain that associates with this phenotype which can serve as predictors of severe epidemics. FUNDING Duke-NUS Khoo Post-doctoral Fellowship Award 2020 (KWKC) and National Medical Research Council of Singapore grants MOH-000524 (OFIRG) (SW) and MOH-OFIRG20nov-0002 (SGV).
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Affiliation(s)
- Kitti Wing Ki Chan
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Amanda Makha Bifani
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Satoru Watanabe
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Milly M Choy
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Eng Eong Ooi
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore; Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, 117545, Singapore.
| | - Subhash G Vasudevan
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore; Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, 117545, Singapore; Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Queensland, 4222, Australia.
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Miller AM, Szalontay L, Bouvier N, Hill K, Ahmad H, Rafailov J, Lee AJ, Rodriguez-Sanchez MI, Yildirim O, Patel A, Bale TA, Benhamida JK, Benayed R, Arcila ME, Donzelli M, Dunkel IJ, Gilheeney SW, Khakoo Y, Kramer K, Sait SF, Greenfield JP, Souweidane MM, Haque S, Mauguen A, Berger MF, Mellinghoff IK, Karajannis MA. Next-generation sequencing of cerebrospinal fluid for clinical molecular diagnostics in pediatric, adolescent and young adult brain tumor patients. Neuro Oncol 2022; 24:1763-1772. [PMID: 35148412 PMCID: PMC9527510 DOI: 10.1093/neuonc/noac035] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Safe sampling of central nervous system tumor tissue for diagnostic purposes may be difficult if not impossible, especially in pediatric patients, and an unmet need exists to develop less invasive diagnostic tests. METHODS We report our clinical experience with minimally invasive molecular diagnostics using a clinically validated assay for sequencing of cerebrospinal fluid (CSF) cell-free DNA (cfDNA). All CSF samples were collected as part of clinical care, and results reported to both clinicians and patients/families. RESULTS We analyzed 64 CSF samples from 45 pediatric, adolescent and young adult (AYA) patients (pediatric = 25; AYA = 20) with primary and recurrent brain tumors across 12 histopathological subtypes including high-grade glioma (n = 10), medulloblastoma (n = 10), pineoblastoma (n = 5), low-grade glioma (n = 4), diffuse leptomeningeal glioneuronal tumor (DLGNT) (n = 4), retinoblastoma (n = 4), ependymoma (n = 3), and other (n = 5). Somatic alterations were detected in 30/64 samples (46.9%) and in at least one sample per unique patient in 21/45 patients (46.6%). CSF cfDNA positivity was strongly associated with the presence of disseminated disease at the time of collection (81.5% of samples from patients with disseminated disease were positive). No association was seen between CSF cfDNA positivity and the timing of CSF collection during the patient's disease course. CONCLUSIONS We identified three general categories where CSF cfDNA testing provided additional relevant diagnostic, prognostic, and/or therapeutic information, impacting clinical assessment and decision making: (1) diagnosis and/or identification of actionable alterations; (2) monitor response to therapy; and (3) tracking tumor evolution. Our findings support broader implementation of clinical CSF cfDNA testing in this population to improve care.
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Affiliation(s)
| | | | - Nancy Bouvier
- Pediatric Translational Medicine Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Katherine Hill
- Pediatric Translational Medicine Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hamza Ahmad
- Pediatric Translational Medicine Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Johnathan Rafailov
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alex J Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - M Irene Rodriguez-Sanchez
- Pediatric Translational Medicine Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Onur Yildirim
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Arti Patel
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tejus A Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maria Donzelli
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ira J Dunkel
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stephen W Gilheeney
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yasmin Khakoo
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kim Kramer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sameer F Sait
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jeffrey P Greenfield
- Department of Pediatrics, Weill Cornell Medical College, New York, New York, USA,Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Neurological Surgery, Weill Cornell Medical College, New York, New York, USA,Department of Neurological Surgery, Columbia University Irving Medical Center, New York, New York, USA
| | - Mark M Souweidane
- Department of Pediatrics, Weill Cornell Medical College, New York, New York, USA,Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Neurological Surgery, Weill Cornell Medical College, New York, New York, USA,Department of Neurological Surgery, Columbia University Irving Medical Center, New York, New York, USA
| | - Sofia Haque
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael F Berger
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ingo K Mellinghoff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Pharmacology, Weill Cornell Medical College, New York, New York, USA
| | - Matthias A Karajannis
- Corresponding Author: Matthias A. Karajannis, MD, MS, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065, USA ()
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Sobhy NM, Armién AG, Pilot J, Singh V, Padhi SK, Muldoon D, Goyal SM, Mor SK. Detection and molecular characterization of astro and bocaviruses in dogs in Minnesota. Comp Immunol Microbiol Infect Dis 2021; 81:101740. [PMID: 34971935 DOI: 10.1016/j.cimid.2021.101740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 10/19/2022]
Abstract
Canine astrovirus (CAstV) and canine bocavirus (CBoV) are involved in cases of mild, and sometimes severe, gastroenteritis in dogs. Fecal samples from two dead dogs with gastroenteritis were received at the University of Minnesota Veterinary Diagnostic Laboratory to determine the cause of death. Small round viruses of 20-35 nm diameter were observed by negative contrast electron microscopy. The samples were subjected to Illumina MiSeq sequencing. Both samples were strongly positive for CAstV; all viral reads were related to CAstV. In addition, sample number 1 had a few reads of CBoV. Two complete sequences of CAstV were identified (6625 and 6627 nt in length) with 95% nt identity. RT-PCR and PCR were used to confirm CAstV and CBoV infections in successive samples of canine gastroenteritis. Sanger sequencing was done on nucleic acids from positive samples. Of a total of ten samples, CAstV and CBoV infections were confirmed in six and eight animals, respectively. Four animals had mixed infection with both viruses. All sequences of ORF1b gene of CAstVs showed closest clusters in phylogenetic tree with 96-100% nucleotide and amino acids identity. On the other hand, identity between VP2 gene of different CBoV strains in this study ranged from 93%- 100%. All strains were located close to each other except the divergent MT078234 strain, which was arranged in a separate branch and was closer to reference strain JN648103/USA/2010. This study highlights the importance of electron microscopy and next generation sequencing for early detection and characterization of viruses associated with dog gastroenteritis.
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Affiliation(s)
- N M Sobhy
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA; Department of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia 44511, Egypt
| | - A G Armién
- California Animal Health and Food Safety Laboratory System, University of California, Davis, CA 95616, USA
| | - J Pilot
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - V Singh
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - S K Padhi
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - D Muldoon
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - S M Goyal
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - S K Mor
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
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Mor SK, Kumar R, Sobhy NM, Singh A, Kakrudi N, Marusak RA, Goyal SM, Porter RE. Enteric Viruses Associated with Mid-growth Turkey Enteritis. Avian Dis 2021; 64:471-477. [PMID: 33347553 DOI: 10.1637/0005-2086-64.4.471] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 06/12/2020] [Indexed: 11/05/2022]
Abstract
Since August 2014, the University of Minnesota Veterinary Diagnostic Laboratory has received cases of turkey enteritis that are clinically different from previously described cases of poult enteritis syndrome and light turkey syndrome. The birds develop dark green and extremely foul-smelling diarrhea starting at 8-10 wk of age, which may last up to 15-16 wk of age. The affected turkey flocks show poor uniformity, and feed conversion and market weights are reduced. Multiple-age farms are affected more often than the single-age farms. Morbidity varies from flock to flock and in some cases reaches 100%. At necropsy, undigested feed with increased mucus is observed in the intestines along with prominent mucosal congestion and/or hemorrhage. Microscopically, lymphocytic infiltrates expand the villi in duodenum and jejunum to form lymphoid follicles, which are often accompanied by heterophils. Next generation sequencing (Illumina Miseq) on a pool of feces from affected birds identified genetic sequences of viruses belonging to Astroviridae, Reoviridae, Picornaviridae, Picobirnaviridae, and Adenoviridae. On testing pools of fecal samples from apparently healthy (16 pools) and affected birds (30 pools), there was a higher viral load in the feces of affected birds. Picobirnavirus was detected only in the affected birds; 20 of 30 pools (66.7%) were positive. These results indicate that a high viral load of turkey picobirnavirus alone, or in association with novel picornaviruses, may be a cause of this new type of turkey enteritis.
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Affiliation(s)
- Sunil K Mor
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108
| | - Rahul Kumar
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108.,U.P. Pt. Deen Dayal Upadhyaya Veterinary Science University and Cattle Research Institute (DUVASU), Mathura, UP 281001, India
| | - Nader M Sobhy
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108
| | - Azad Singh
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108
| | - Nima Kakrudi
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108
| | | | - Sagar M Goyal
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108
| | - Robert E Porter
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108
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Ramakrishna G, Kaur P, Nigam D, Chaduvula PK, Yadav S, Talukdar A, Singh NK, Gaikwad K. Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits. BMC Plant Biol 2018; 18:141. [PMID: 29986650 PMCID: PMC6038289 DOI: 10.1186/s12870-018-1341-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 06/05/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Water permeability governed by seed coat is a major facet of seed crops, especially soybean, whose seeds lack physiological dormancy and experience rapid deterioration in seed viability under prolonged storage. Moreover, the physiological and chemical characteristics of soybean seeds are known to vary with seed coat color. Thus, to underpin the genes controlling water permeability in soybean seeds, we carried out an in-depth characterization of the associated genomic variation. RESULTS In the present study, we have analyzed genomic variation between cultivated soybean and its wild progenitor with implications on seed permeability, a trait related to seed storability. Whole genome resequencing of G.max and G. soja, identified SNPs and InDels which were further characterized on the basis of their genomic location and impact on gene expression. Chromosomal density distribution of the variation was assessed across the genome and genes carrying SNPs and InDels were characterized into different metabolic pathways. Seed hardiness is a complex trait that is affected by the allelic constitution of a genetic locus as well as by a tricky web of plant hormone interactions. Seven genes that hold a probable role in the determination of seed permeability were selected and their expression differences at different stages of water imbibition were analyzed. Variant interaction network derived 205 downstream interacting partners of 7 genes confirmed their role in seed related traits. Interestingly, genes encoding for Type I- Inositol polyphosphate 5 phosphatase1 and E3 Ubiquitin ligase could differentiate parental genotypes, revealed protein conformational deformations and were found to segregate among RILs in coherence with their permeability scores. The 2 identified genes, thus showed a preliminary association with the desirable permeability characteristics. CONCLUSION In the light of above outcomes, 2 genes were identified that revealed preliminary, but a relevant association with soybean seed permeability trait and hence could serve as a primary material for understanding the molecular pathways controlling seed permeability traits in soybean.
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Affiliation(s)
- G. Ramakrishna
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Parampreet Kaur
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Deepti Nigam
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Pavan K. Chaduvula
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Sangita Yadav
- ICAR- IARI, Division of Seed Science and Technology, Pusa Campus, New Delhi, 110012 India
| | - Akshay Talukdar
- ICAR- IARI, Division of Genetics, Pusa Campus, New Delhi, India
| | - Nagendra Kumar Singh
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Kishor Gaikwad
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
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Koo H, Hakim JA, Morrow CD, Eipers PG, Davila A, Andersen DT, Bej AK. Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica. J Microbiol Methods 2017; 140:15-22. [PMID: 28655556 DOI: 10.1016/j.mimet.2017.06.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 01/01/2023]
Abstract
In this study, using NextGen sequencing of the collective 16S rRNA genes obtained from two sets of samples collected from Lake Obersee, Antarctica, we compared and contrasted two bioinformatics tools, PICRUSt and Tax4Fun. We then developed an R script to assess the taxonomic and predictive functional profiles of the microbial communities within the samples. Taxa such as Pseudoxanthomonas, Planctomycetaceae, Cyanobacteria Subsection III, Nitrosomonadaceae, Leptothrix, and Rhodobacter were exclusively identified by Tax4Fun that uses SILVA database; whereas PICRUSt that uses Greengenes database uniquely identified Pirellulaceae, Gemmatimonadetes A1-B1, Pseudanabaena, Salinibacterium and Sinobacteraceae. Predictive functional profiling of the microbial communities using Tax4Fun and PICRUSt separately revealed common metabolic capabilities, while also showing specific functional IDs not shared between the two approaches. Combining these functional predictions using a customized R script revealed a more inclusive metabolic profile, such as hydrolases, oxidoreductases, transferases; enzymes involved in carbohydrate and amino acid metabolisms; and membrane transport proteins known for nutrient uptake from the surrounding environment. Our results present the first molecular-phylogenetic characterization and predictive functional profiles of the microbial mat communities in Lake Obersee, while demonstrating the efficacy of combining both the taxonomic assignment information and functional IDs using the R script created in this study for a more streamlined evaluation of predictive functional profiles of microbial communities.
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Affiliation(s)
- Hyunmin Koo
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Casey D Morrow
- Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Peter G Eipers
- Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alfonso Davila
- NASA Ames Research Center, MS 245-3, Moffett Field, CA, USA
| | | | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
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Koo H, Hakim JA, Powell ML, Kumar R, Eipers PG, Morrow CD, Crowley M, Lefkowitz EJ, Watts SA, Bej AK. Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet. J Microbiol Methods 2017; 135:69-76. [PMID: 28167213 PMCID: PMC5909692 DOI: 10.1016/j.mimet.2017.01.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [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: 12/14/2016] [Revised: 01/28/2017] [Accepted: 01/28/2017] [Indexed: 01/08/2023]
Abstract
In this study, we report the gut microbial composition and predictive functional profiles of zebrafish, Danio rerio, fed with a control formulated diet (CFD), and a gluten formulated diet (GFD) using a metagenomics approach and bioinformatics tools. The microbial communities of the GFD-fed D. rerio displayed heightened abundances of Legionellales, Rhizobiaceae, and Rhodobacter, as compared to the CFD-fed counterparts. Predicted metagenomics of microbial communities (PICRUSt) in GFD-fed D. rerio showed KEGG functional categories corresponding to bile secretion, secondary bile acid biosynthesis, and the metabolism of glycine, serine, and threonine. The CFD-fed D. rerio exhibited KEGG functional categories of bacteria-mediated cobalamin biosynthesis, which was supported by the presence of cobalamin synthesizers such as Bacteroides and Lactobacillus. Though these bacteria were absent in GFD-fed D. rerio, a comparable level of the cobalamin biosynthesis KEGG functional category was observed, which could be contributed by the compensatory enrichment of Cetobacterium. Based on these results, we conclude D. rerio to be a suitable alternative animal model for the use of a targeted metagenomics approach along with bioinformatics tools to further investigate the relationship between the gluten diet and microbiome profile in the gut ecosystem leading to gastrointestinal diseases and other undesired adverse health effects.
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Affiliation(s)
- Hyunmin Koo
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mickie L Powell
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ranjit Kumar
- Biomedical Informatics, Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Peter G Eipers
- Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Casey D Morrow
- Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michael Crowley
- Heflin Center for Genomic Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Elliot J Lefkowitz
- Biomedical Informatics, Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stephen A Watts
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
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10
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Hemphill DD, McIlwraith CW, Slayden RA, Samulski RJ, Goodrich LR. Adeno-associated virus gene therapy vector scAAVIGF-I for transduction of equine articular chondrocytes and RNA-seq analysis. Osteoarthritis Cartilage 2016; 24:902-11. [PMID: 26706703 DOI: 10.1016/j.joca.2015.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 11/08/2015] [Accepted: 12/01/2015] [Indexed: 02/02/2023]
Abstract
OBJECTIVE IGF-I is one of several anabolic factors being investigated for the treatment of osteoarthritis (OA). Due to the short biological half-life, extended administration is required for more robust cartilage healing. Here we create a self-complimentary adeno-associated virus (AAV) gene therapy vector utilizing the transgene for IGF-I. DESIGN Various biochemical assays were performed to investigate the cellular response to scAAVIGF-I treatment vs an scAAVGFP positive transduction control and a negative for transduction control culture. RNA-sequencing analysis was also performed to establish a differential regulation profile of scAAVIGF-I transduced chondrocytes. RESULTS Biochemical analyses indicated an average media IGF-I concentration of 608 ng/ml in the scAAVIGF-I transduced chondrocytes. This increase in IGF-I led to increased expression of collagen type II and aggrecan and increased protein concentrations of cellular collagen type II and media glycosaminoglycan vs both controls. RNA-seq revealed a global regulatory pattern consisting of 113 differentially regulated GO categories including those for chondrocyte and cartilage development and regulation of apoptosis. CONCLUSIONS This research substantiates that scAAVIGF-I gene therapy vector increased production of IGF-I to clinically relevant levels with a biological response by chondrocytes conducive to increased cartilage healing. The RNA-seq further established a set of differentially expressed genes and gene ontologies induced by the scAAVIGF-I vector while controlling for AAV infection. This dataset provides a static representation of the cellular transcriptome that, while only consisting of one time point, will allow for further gene expression analyses to compare additional cartilage healing therapeutics or a transient cellular response.
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Affiliation(s)
- D D Hemphill
- Orthopaedic Research Center, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523, USA.
| | - C W McIlwraith
- Orthopaedic Research Center, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523, USA.
| | - R A Slayden
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
| | - R J Samulski
- University of North Carolina Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - L R Goodrich
- Orthopaedic Research Center, College of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523, USA.
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11
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Abstract
The concept of proteogenomics has emerged rapidly as a valuable approach to integrate mass spectrometry-derived proteomic data with genomic and transcriptomic data. It is used to harness the full potential of the former dataset in the discovery of potential biomarkers, therapeutic targets and novel proteins associated with various biological processes including diseases. Proteogenomic strategies have been successfully utilized to identify novel genes and redefine annotation of existing gene models in various genomes. In recent years, this approach has been extended to the field of cancer biology to unravel complexities in the tumor genomes and proteomes. Standard proteomics workflows employing translated cancer genomes and transcriptomes can potentially identify peptides from mutant proteins, splice variants and fusion proteins in the tumor proteome, which in addition to the currently available biomarker panels can serve as potential diagnostic and prognostic biomarkers, besides having therapeutic utility. This review focuses on the role of proteogenomics to understand cancer biology.
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Affiliation(s)
- Yashwanth Subbannayya
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India
| | - Sneha M Pinto
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India
| | - Harsha Gowda
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India
| | - T S Keshava Prasad
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India.,c NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre , National Institute of Mental Health and Neurosciences , Bangalore , India
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12
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Boles RG, Hornung HA, Moody AE, Ortiz TB, Wong SA, Eggington JM, Stanley CM, Gao M, Zhou H, McLaughlin S, Zare AS, Sheldon KM, Skolnick J, McKernan KJ. Hurt, tired and queasy: Specific variants in the ATPase domain of the TRAP1 mitochondrial chaperone are associated with common, chronic "functional" symptomatology including pain, fatigue and gastrointestinal dysmotility. Mitochondrion 2015; 23:64-70. [PMID: 26022780 DOI: 10.1016/j.mito.2015.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 05/15/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
Abstract
Functional disorders are common conditions with a substantial impact on a patients' wellbeing, and can be diagnostically elusive. There are bidirectional associations between functional disorders and mitochondrial dysfunction. In this study, provided clinical information and the exon sequence of the TRAP1 mitochondrial chaperone were retrospectively reviewed with a focus on the functional categories of chronic pain, fatigue and gastrointestinal dysmotility. Very-highly conserved TRAP1 variants were identified in 73 of 930 unrelated patients. Functional symptomatology is strongly associated with specific variants in the ATPase binding pocket. In particular, the combined presence of all three functional categories is strongly associated with p.Ile253Val (OR 7.5, P = 0.0001) and with two other interacting variants (OR 18, P = 0.0005). Considering a 1-2% combined variant prevalence and high odds ratios, these variants may be an important factor in the etiology of functional symptomatology.
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Affiliation(s)
- Richard G Boles
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Holly A Hornung
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Alastair E Moody
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Thomas B Ortiz
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Stacey A Wong
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Julie M Eggington
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Christine M Stanley
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Mu Gao
- Center for the Study of Systems Biology, Georgia Institute of Technology, 250 14th St, Atlanta, GA 30318, United States
| | - Hongyi Zhou
- Center for the Study of Systems Biology, Georgia Institute of Technology, 250 14th St, Atlanta, GA 30318, United States
| | - Stephen McLaughlin
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Amir S Zare
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Katherine M Sheldon
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, Georgia Institute of Technology, 250 14th St, Atlanta, GA 30318, United States
| | - Kevin J McKernan
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
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13
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Abstract
Humans are exposed to thousands of chemicals with inadequate toxicological data. Advances in computational toxicology, robotic high throughput screening (HTS), and genome-wide expression have been integrated into the Tox21 program to better predict the toxicological effects of chemicals. Tox21 is a collaboration among US government agencies initiated in 2008 that aims to shift chemical hazard assessment from traditional animal toxicology to target-specific, mechanism-based, biological observations using in vitro assays and lower organism models. HTS uses biocomputational methods for probing thousands of chemicals in in vitro assays for gene-pathway response patterns predictive of adverse human health outcomes. In 1999, NIEHS began exploring the application of toxicogenomics to toxicology and recent advances in NextGen sequencing should greatly enhance the biological content obtained from HTS platforms. We foresee an intersection of new technologies in toxicogenomics and HTS as an innovative development in Tox21. Tox21 goals, priorities, progress, and challenges will be reviewed.
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Affiliation(s)
- B Alex Merrick
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Richard S Paules
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Raymond R Tice
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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14
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Geniez S, Foster JM, Kumar S, Moumen B, Leproust E, Hardy O, Guadalupe M, Thomas SJ, Boone B, Hendrickson C, Bouchon D, Grève P, Slatko BE. Targeted genome enrichment for efficient purification of endosymbiont DNA from host DNA. Symbiosis 2013; 58:201-207. [PMID: 23482460 PMCID: PMC3589621 DOI: 10.1007/s13199-012-0215-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 12/10/2012] [Indexed: 12/16/2022]
Abstract
Wolbachia endosymbionts are widespread in arthropods and are generally considered reproductive parasites, inducing various phenotypes including cytoplasmic incompatibility, parthenogenesis, feminization and male killing, which serve to promote their spread through populations. In contrast, Wolbachia infecting filarial nematodes that cause human diseases, including elephantiasis and river blindness, are obligate mutualists. DNA purification methods for efficient genomic sequencing of these unculturable bacteria have proven difficult using a variety of techniques. To efficiently capture endosymbiont DNA for studies that examine the biology of symbiosis, we devised a parallel strategy to an earlier array-based method by creating a set of SureSelect™ (Agilent) 120-mer target enrichment RNA oligonucleotides ("baits") for solution hybrid selection. These were designed from Wolbachia complete and partial genome sequences in GenBank and were tiled across each genomic sequence with 60 bp overlap. Baits were filtered for homology against host genomes containing Wolbachia using BLAT and sequences with significant host homology were removed from the bait pool. Filarial parasite Brugia malayi DNA was used as a test case, as the complete sequence of both Wolbachia and its host are known. DNA eluted from capture was size selected and sequencing samples were prepared using the NEBNext® Sample Preparation Kit. One-third of a 50 nt paired-end sequencing lane on the HiSeq™ 2000 (Illumina) yielded 53 million reads and the entirety of the Wolbachia genome was captured. We then used the baits to isolate more than 97.1 % of the genome of a distantly related Wolbachia strain from the crustacean Armadillidium vulgare, demonstrating that the method can be used to enrich target DNA from unculturable microbes over large evolutionary distances.
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Affiliation(s)
- Sandrine Geniez
- New England Biolabs, Inc., Ipswich, MA 01938 USA ; Écologie et Biologie des Interactions, Équipe Écologie, Évolution, Symbiose, University of Poitiers UMR CNRS 7267, 86022 Poitiers, France
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