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Nargar K, O’Hara K, Mertin A, Bent SJ, Nauheimer L, Simpson L, Zimmer H, Molloy BPJ, Clements MA. Evolutionary Relationships and Range Evolution of Greenhood Orchids (Subtribe Pterostylidinae): Insights From Plastid Phylogenomics. Front Plant Sci 2022; 13:912089. [PMID: 35845679 PMCID: PMC9277221 DOI: 10.3389/fpls.2022.912089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Australia harbours a rich and highly endemic orchid flora with over 90% of native species found nowhere else. However, little is known about the assembly and evolution of Australia's orchid flora. Here, we used a phylogenomic approach to infer evolutionary relationships, divergence times and range evolution in Pterostylidinae (Orchidoideae), the second largest subtribe in the Australian orchid flora, comprising the genera Pterostylis and Achlydosa. Phylogenetic analysis of 75 plastid genes provided well-resolved and supported phylogenies. Intrageneric relationships in Pterostylis were clarified and monophyly of eight of 10 sections supported. Achlydosa was found to not form part of Pterostylidinae and instead merits recognition at subtribal level, as Achlydosinae. Pterostylidinae were inferred to have originated in eastern Australia in the early Oligocene, coinciding with the complete separation of Australia from Antarctica and the onset of the Antarctic Circumpolar Current, which led to profound changes in the world's climate. Divergence of all major lineages occurred during the Miocene, accompanied by increased aridification and seasonality of the Australian continent, resulting in strong vegetational changes from rainforest to more open sclerophyllous vegetation. The majority of extant species were inferred to have originated in the Quaternary, from the Pleistocene onwards. The rapid climatic oscillations during the Pleistocene may have acted as important driver of speciation in Pterostylidinae. The subtribe underwent lineage diversification mainly within its ancestral range, in eastern Australia. Long-distance dispersals to southwest Australia commenced from the late Miocene onwards, after the establishment of the Nullarbor Plain, which constitutes a strong edaphic barrier to mesic plants. Range expansions from the mesic into the arid zone of eastern Australia (Eremaean region) commenced from the early Pleistocene onwards. Extant distributions of Pterostylidinae in other Australasian regions, such as New Zealand and New Caledonia, are of more recent origin, resulting from long-distance dispersals from the Pliocene onwards. Temperate eastern Australia was identified as key source area for dispersals to other Australasian regions.
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Affiliation(s)
- Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Kate O’Hara
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Allison Mertin
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Stephen J. Bent
- DATA61, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
| | - Lars Nauheimer
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Lalita Simpson
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Heidi Zimmer
- Centre for Australian National Biodiversity Research (Joint Venture Between Parks Australia and CSIRO), Canberra, ACT, Australia
| | - Brian P. J. Molloy
- Allan Herbarium, Manaaki Whenua – Landcare Research, Lincoln, New Zealand
| | - Mark A. Clements
- Centre for Australian National Biodiversity Research (Joint Venture Between Parks Australia and CSIRO), Canberra, ACT, Australia
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2
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Appleyard SA, Maher S, Pogonoski JJ, Bent SJ, Chua XY, McGrath A. Assessing DNA for fish identifications from reference collections: the good, bad and ugly shed light on formalin fixation and sequencing approaches. J Fish Biol 2021; 98:1421-1432. [PMID: 33484178 DOI: 10.1111/jfb.14687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Natural history collections are repositories of biodiversity and are potentially used by molecular ecologists for comparative taxonomic, phylogenetic, biogeographic and forensic purposes. Specimens in fish collections are preserved using a combination of methods with many fixed in formalin and then preserved in ethanol for long-term storage. Formalin fixation damages DNA, thereby limiting genetic analyses. In this study, the authors compared the DNA barcoding and identification success for frozen and formalin-fixed tissues obtained from specimens in the CSIRO Australian National Fish Collection. They studied 230 samples from fishes (consisting of >160 fish species). An optimized formalin-fixed, paraffin-embedded DNA extraction method resulted in usable DNA from degraded tissues. Four mini barcoding assays of the mitochondrial DNA (mtDNA) were characterized with Sanger and Illumina amplicon sequencing. In the good quality DNA (without exposure to formalin), up to 88% of the specimens were correctly matched at the species level using the cytochrome oxidase subunit 1 (COI) mini barcodes, whereas up to 58% of the specimens exposed to formalin for less than 8 weeks were correctly identified to species. In contrast, 16S primers provided higher amplification success with formalin-exposed tissues, although the COI gene was more successful for identification. Importantly, the authors found that DNA of a certain size and quality can be amplified and sequenced despite exposure to formalin, and Illumina sequencing provided them with greater power of resolution for taxa identification even when there was little DNA present. Overall, within parameter constraints, this study highlights the possibilities of recovering DNA barcodes for identification from formalin-fixed fish specimens, and the authors provide guidelines for when successful identification could be expected.
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Affiliation(s)
- Sharon A Appleyard
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Tasmania, Australia
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
| | - Safia Maher
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Tasmania, Australia
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
| | - John J Pogonoski
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Tasmania, Australia
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
| | - Stephen J Bent
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
- Data 61, CSIRO, Brisbane, Queensland, Australia
| | - Xin-Yi Chua
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
- Data 61, CSIRO, Brisbane, Queensland, Australia
- School of Electrical Engineering and Computer Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Annette McGrath
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
- Data 61, CSIRO, Brisbane, Queensland, Australia
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Helman G, Lajoie BR, Crawford J, Takanohashi A, Walkiewicz M, Dolzhenko E, Gross AM, Gainullin VG, Bent SJ, Jenkinson EM, Ferdinandusse S, Waterham HR, Dorboz I, Bertini E, Miyake N, Wolf NI, Abbink TEM, Kirwin SM, Tan CM, Hobson GM, Guo L, Ikegawa S, Pizzino A, Schmidt JL, Bernard G, Schiffmann R, van der Knaap MS, Simons C, Taft RJ, Vanderver A. Genome sequencing in persistently unsolved white matter disorders. Ann Clin Transl Neurol 2020; 7:144-152. [PMID: 31912665 PMCID: PMC6952322 DOI: 10.1002/acn3.50957] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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] [Received: 10/01/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 01/01/2023] Open
Abstract
Genetic white matter disorders have heterogeneous etiologies and overlapping clinical presentations. We performed a study of the diagnostic efficacy of genome sequencing in 41 unsolved cases with prior exome sequencing, resolving an additional 14 from an historical cohort (n = 191). Reanalysis in the context of novel disease-associated genes and improved variant curation and annotation resolved 64% of cases. The remaining diagnoses were directly attributable to genome sequencing, including cases with small and large copy number variants (CNVs) and variants in deep intronic and technically difficult regions. Genome sequencing, in combination with other methodologies, achieved a diagnostic yield of 85% in this retrospective cohort.
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Affiliation(s)
- Guy Helman
- Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | | | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Asako Takanohashi
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Marzena Walkiewicz
- Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, Australia
| | | | | | | | - Stephen J Bent
- Data61, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia
| | - Emma M Jenkinson
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Imen Dorboz
- INSERM UMR 1141, DHU PROTECT, Université Paris Diderot- Sorbonne, Paris Cité, France
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesu' Children's Hospital, Rome, Italy.,Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, 00146, Rome, Italy
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Nicole I Wolf
- Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Truus E M Abbink
- Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Susan M Kirwin
- Molecular Diagnostics Laboratory, Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Christina M Tan
- Molecular Diagnostics Laboratory, Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Grace M Hobson
- Molecular Diagnostics Laboratory, Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Long Guo
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Amy Pizzino
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Johanna L Schmidt
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Genevieve Bernard
- Departments of Neurology and Neurosurgery, Pediatrics, and Human Genetics, McGill University, Montreal, Canada.,Division of Medical Genetics, Montreal Children's Hospital, McGill University Health Center, Montreal, Canada.,Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Raphael Schiffmann
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, Texas
| | - Marjo S van der Knaap
- Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Amsterdam, The Netherlands.,Department of Functional Genomics, Amsterdam Neuroscience, VU University, Amsterdam, the Netherlands
| | - Cas Simons
- Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | | | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Yan H, Helman G, Murthy SE, Ji H, Crawford J, Kubisiak T, Bent SJ, Xiao J, Taft RJ, Coombs A, Wu Y, Pop A, Li D, de Vries LS, Jiang Y, Salomons GS, van der Knaap MS, Patapoutian A, Simons C, Burmeister M, Wang J, Wolf NI. Heterozygous Variants in the Mechanosensitive Ion Channel TMEM63A Result in Transient Hypomyelination during Infancy. Am J Hum Genet 2019; 105:996-1004. [PMID: 31587869 DOI: 10.1016/j.ajhg.2019.09.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [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: 07/04/2019] [Accepted: 09/09/2019] [Indexed: 01/05/2023] Open
Abstract
Mechanically activated (MA) ion channels convert physical forces into electrical signals. Despite the importance of this function, the involvement of mechanosensitive ion channels in human disease is poorly understood. Here we report heterozygous missense mutations in the gene encoding the MA ion channel TMEM63A that result in an infantile disorder resembling a hypomyelinating leukodystrophy. Four unrelated individuals presented with congenital nystagmus, motor delay, and deficient myelination on serial scans in infancy, prompting the diagnosis of Pelizaeus-Merzbacher (like) disease. Genomic sequencing revealed that all four individuals carry heterozygous missense variants in the pore-forming domain of TMEM63A. These variants were confirmed to have arisen de novo in three of the four individuals. While the physiological role of TMEM63A is incompletely understood, it is highly expressed in oligodendrocytes and it has recently been shown to be a MA ion channel. Using patch clamp electrophysiology, we demonstrated that each of the modeled variants result in strongly attenuated stretch-activated currents when expressed in naive cells. Unexpectedly, the clinical evolution of all four individuals has been surprisingly favorable, with substantial improvements in neurological signs and developmental progression. In the three individuals with follow-up scans after 4 years of age, the myelin deficit had almost completely resolved. Our results suggest a previously unappreciated role for mechanosensitive ion channels in myelin development.
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Affiliation(s)
- Huifang Yan
- Department of Pediatrics, Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing 100871, China; Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA; Joint International Research Center of Translational and Clinical Research, Beijing 100871, China
| | - Guy Helman
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Melbourne, VIC 3052, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Swetha E Murthy
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037 USA
| | - Haoran Ji
- Department of Pediatrics, Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing 100871, China; Children's Hospital of Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Kubisiak
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stephen J Bent
- Data61, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD 4067, Australia
| | - Jiangxi Xiao
- Department of Radiology, Peking University First Hospital, Beijing 100871, China
| | | | - Adam Coombs
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037 USA
| | - Ye Wu
- Department of Pediatrics, Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing 100871, China
| | - Ana Pop
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam 1081 HV, the Netherlands; Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, Amsterdam 1081 HV, the Netherlands
| | - Dongxiao Li
- Department of Pediatrics, Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing 100871, China; Henan Provincial Key Laboratory of Children's Genetic and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Linda S de Vries
- Department of Neonatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht 3584 EA, the Netherlands; UMC Utrecht Brain Center, Utrecht 3584 CG, the Netherlands
| | - Yuwu Jiang
- Department of Pediatrics, Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing 100871, China; Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Peking University, Beijing 100871, China
| | - Gajja S Salomons
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam 1081 HV, the Netherlands; Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, Amsterdam 1081 HV, the Netherlands; Department of Genetic Metabolic Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands; Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Amsterdam 1081 HV, the Netherlands
| | - Marjo S van der Knaap
- Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Amsterdam 1081 HV, the Netherlands; Department of Functional Genomics, Amsterdam Neuroscience, VU University, Amsterdam 1081 HV, the Netherlands
| | - Ardem Patapoutian
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037 USA
| | - Cas Simons
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Melbourne, VIC 3052, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Margit Burmeister
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA; Departments of Computational Medicine & Bioinformatics, Psychiatry and Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jingmin Wang
- Department of Pediatrics, Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing 100871, China; Joint International Research Center of Translational and Clinical Research, Beijing 100871, China; Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Peking University, Beijing 100871, China
| | - Nicole I Wolf
- Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Amsterdam 1081 HV, the Netherlands.
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Simons C, Dyment D, Bent SJ, Crawford J, D'Hooghe M, Kohlschütter A, Venkateswaran S, Helman G, Poll-The BT, Makowski CC, Ito Y, Kernohan K, Hartley T, Waisfisz Q, Taft RJ, van der Knaap MS, Wolf NI. A recurrent de novo mutation in TMEM106B causes hypomyelinating leukodystrophy. Brain 2019; 140:3105-3111. [PMID: 29186371 DOI: 10.1093/brain/awx314] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/05/2017] [Indexed: 12/28/2022] Open
Abstract
Hypomyelinating leukodystrophies are a heterogeneous group of disorders with a clinical presentation that often includes early-onset nystagmus, ataxia and spasticity and a wide range of severity. Using next-generation sequencing techniques and GeneMatcher, we identified four unrelated patients with brain hypomyelination, all with the same recurrent dominant mutation, c.754G>A p.(Asp252Asn), in TMEM106B. The mutation was confirmed as de novo in three of the cases, and the mildly affected father of the fourth affected individual was confirmed as mosaic for this variant. The protein encoded by TMEM106B is poorly characterized but is reported to have a role in regulation of lysosomal trafficking. Polymorphisms in TMEM106B are thought to modify disease onset in frontotemporal dementia, but its relation to myelination is not understood. Clinical presentation in three of the four patients is remarkably benign compared to other hypomyelinating disorders, with congenital nystagmus and mild motor delay. These findings add TMEM106B to the growing list of genes causing hypomyelinating disorders and emphasize the essential role lysosomes play in myelination.
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Affiliation(s)
- Cas Simons
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Stephen J Bent
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - Joanna Crawford
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - Marc D'Hooghe
- Department of Neurology, General Hospital Sint-Jan, Brugge, Belgium
| | - Alfried Kohlschütter
- Department of Paediatrics, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Sunita Venkateswaran
- Division of Neurology, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Guy Helman
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - Bwee-Tien Poll-The
- Department of Child Neurology, Academic Medical Center, Amsterdam, The Netherlands
| | | | - Yoko Ito
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Kristin Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Quinten Waisfisz
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Ryan J Taft
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia.,Illumina Inc, San Diego, California, USA
| | | | - Marjo S van der Knaap
- Department of Child Neurology, VU University Medical Center, and Amsterdam Neuroscience, Amsterdam, The Netherlands.,Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - Nicole I Wolf
- Department of Child Neurology, VU University Medical Center, and Amsterdam Neuroscience, Amsterdam, The Netherlands
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6
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Helman G, Sharma S, Crawford J, Patra B, Jain P, Bent SJ, Urtizberea JA, Saran RK, Taft RJ, van der Knaap MS, Simons C. Leukoencephalopathy due to variants in GFPT1-associated congenital myasthenic syndrome. Neurology 2019; 92:e587-e593. [PMID: 30635494 DOI: 10.1212/wnl.0000000000006886] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/06/2018] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVE To determine the molecular etiology of disease in 4 individuals from 2 unrelated families who presented with proximal muscle weakness and features suggestive of mitochondrial disease. METHODS Clinical information and neuroimaging were reviewed. Genome sequencing was performed on affected individuals and biological parents. RESULTS All affected individuals presented with muscle weakness and difficulty walking. In one family, both children had neonatal respiratory distress while the other family had 2 children with episodic deteriorations. In each family, muscle biopsy demonstrated ragged red fibers. MRI was suggestive of a mitochondrial leukoencephalopathy, with extensive deep cerebral white matter T2 hyperintense signal and selective involvement of the middle blade of the corpus callosum. Through genome sequencing, homozygous GFPT1 missense variants were identified in the affected individuals of each family. The variants detected (p.Arg14Leu and p.Thr151Lys) are absent from population databases and predicted to be damaging by in silico prediction tools. Following the genetic diagnosis, nerve conduction studies were performed and demonstrated a decremental response to repetitive nerve stimulation, confirming the diagnosis of myasthenia. Treatment with pyridostigmine was started in one family with favorable response. CONCLUSIONS GFPT1 encodes a widely expressed protein that controls the flux of glucose into the hexosamine-biosynthesis pathway that produces precursors for glycosylation of proteins. GFPT1 variants and defects in other enzymes of this pathway have previously been associated with congenital myasthenia. These findings identify leukoencephalopathy as a previously unrecognized phenotype in GFPT1-related disease and suggest that mitochondrial dysfunction could contribute to this disorder.
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Affiliation(s)
- Guy Helman
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Suvasini Sharma
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Joanna Crawford
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Bijoy Patra
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Puneet Jain
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Stephen J Bent
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - J Andoni Urtizberea
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Ravindra K Saran
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Ryan J Taft
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Marjo S van der Knaap
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands.
| | - Cas Simons
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands.
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7
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Miyake N, Wolf NI, Cayami FK, Crawford J, Bley A, Bulas D, Conant A, Bent SJ, Gripp KW, Hahn A, Humphray S, Kimura-Ohba S, Kingsbury Z, Lajoie BR, Lal D, Micha D, Pizzino A, Sinke RJ, Sival D, Stolte-Dijkstra I, Superti-Furga A, Ulrick N, Taft RJ, Ogata T, Ozono K, Matsumoto N, Neubauer BA, Simons C, Vanderver A. X-linked hypomyelination with spondylometaphyseal dysplasia (H-SMD) associated with mutations in AIFM1. Neurogenetics 2017; 18:185-194. [PMID: 28842795 PMCID: PMC5705759 DOI: 10.1007/s10048-017-0520-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [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: 03/20/2017] [Accepted: 08/04/2017] [Indexed: 01/12/2023]
Abstract
An X-linked condition characterized by the combination of hypomyelinating leukodystrophy and spondylometaphyseal dysplasia (H-SMD) has been observed in only four families, with linkage to Xq25-27, and recent genetic characterization in two families with a common AIFM1 mutation. In our study, 12 patients (6 families) with H-SMD were identified and underwent comprehensive assessment accompanied by whole-exome sequencing (WES). Pedigree analysis in all families was consistent with X-linked recessive inheritance. Presentation typically occurred between 12 and 36 months. In addition to the two disease-defining features of spondylometaphyseal dysplasia and hypomyelination on MRI, common clinical signs and symptoms included motor deterioration, spasticity, tremor, ataxia, dysarthria, cognitive defects, pulmonary hypertension, nystagmus, and vision loss due to retinopathy. The course of the disease was slowly progressive. All patients had maternally inherited or de novo mutations in or near exon 7 of AIFM1, within a region of 70 bp, including synonymous and intronic changes. AIFM1 mutations have previously been associated with neurologic presentations as varied as intellectual disability, hearing loss, neuropathy, and striatal necrosis, while AIFM1 mutations in this small region present with a distinct phenotype implicating bone. Analysis of cell lines derived from four patients identified significant reductions in AIFM1 mRNA and protein levels in osteoblasts. We hypothesize that AIFM1 functions in bone metabolism and myelination and is responsible for the unique phenotype in this condition.
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Affiliation(s)
- Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Nicole I Wolf
- Department of Child Neurology, and Amsterdam Neuroscience, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.
| | - Ferdy K Cayami
- Department of Child Neurology, and Amsterdam Neuroscience, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.,Department of Clinical Genetics, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.,Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Annette Bley
- University Children's Hospital, University Medical Center Hamburg Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Dorothy Bulas
- Department of Diagnostic Imaging and Radiology, Children's National Medical Center, Washington, DC, USA
| | - Alex Conant
- Department of Neurology, Children's National Medical Center, Suite 4800, Washington, DC, USA
| | - Stephen J Bent
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Karen W Gripp
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Andreas Hahn
- Department of Pediatric Neurology, Univ.-Klinikum Giessen/Marburg; Standort Giessen, Feulgenstr. 12, 35389, Giessen, Germany
| | - Sean Humphray
- Chesterford Research Park, Illumina, Inc., Little Chesterford, CB10 1XL, UK
| | - Shihoko Kimura-Ohba
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Zoya Kingsbury
- Chesterford Research Park, Illumina, Inc., Little Chesterford, CB10 1XL, UK
| | | | - Dennis Lal
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, USA
| | - Dimitra Micha
- Department of Clinical Genetics, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
| | - Amy Pizzino
- Department of Neurology, Children's National Medical Center, Suite 4800, Washington, DC, USA
| | - Richard J Sinke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Deborah Sival
- Department of Child Neurology, University Hospital Groningen, Groningen, Netherlands
| | - Irene Stolte-Dijkstra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois (CHUV), University of Lausanne, Lausanne, Switzerland
| | - Nicole Ulrick
- Department of Neurology, Children's National Medical Center, Suite 4800, Washington, DC, USA
| | - Ryan J Taft
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.,Illumina, Inc, San Diego, CA, USA.,George Washington University School of Medicine, Washington, DC, USA
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - Keiichi Ozono
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Bernd A Neubauer
- Department of Pediatric Neurology, Univ.-Klinikum Giessen/Marburg; Standort Giessen, Feulgenstr. 12, 35389, Giessen, Germany
| | - Cas Simons
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Adeline Vanderver
- Department of Neurology, Children's National Medical Center, Suite 4800, Washington, DC, USA.,Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois (CHUV), University of Lausanne, Lausanne, Switzerland.,Children's Hospital of Philadelphia, Philadelphia, PA, USA
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8
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Rynkiewicz EC, Brown J, Tufts DM, Huang CI, Kampen H, Bent SJ, Fish D, Diuk-Wasser MA. Closely-related Borrelia burgdorferi (sensu stricto) strains exhibit similar fitness in single infections and asymmetric competition in multiple infections. Parasit Vectors 2017; 10:64. [PMID: 28166814 PMCID: PMC5292797 DOI: 10.1186/s13071-016-1964-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 08/23/2016] [Accepted: 12/30/2016] [Indexed: 11/10/2022] Open
Abstract
Background Wild hosts are commonly co-infected with complex, genetically diverse, pathogen communities. Competition is expected between genetically or ecologically similar pathogen strains which may influence patterns of coexistence. However, there is little data on how specific strains of these diverse pathogen species interact within the host and how this impacts pathogen persistence in nature. Ticks are the most common disease vector in temperate regions with Borrelia burgdorferi, the causative agent of Lyme disease, being the most common vector-borne pathogen in North America. Borrelia burgdorferi is a pathogen of high public health concern and there is significant variation in infection phenotype between strains, which influences predictions of pathogen dynamics and spread. Methods In a laboratory experiment, we investigated whether two closely-related strains of B. burgdorferi (sensu stricto) showed similar transmission phenotypes, how the transmission of these strains changed when a host was infected with one strain, re-infected with the same strain, or co-infected with two strains. Ixodes scapularis, the black-legged tick, nymphs were used to sequentially infect laboratory-bred Peromyscus leucopus, white-footed mice, with one strain only, homologous infection with the same stain, or heterologous infection with both strains. We used the results of this laboratory experiment to simulate long-term persistence and maintenance of each strain in a simple simulation model. Results Strain LG734 was more competitive than BL206, showing no difference in transmission between the heterologous infection groups and single-infection controls, while strain BL206 transmission was significantly reduced when strain LG734 infected first. The results of the model show that this asymmetry in competition could lead to extinction of strain BL206 unless there was a tick-to-host transmission advantage to this less competitive strain. Conclusions This asymmetric competitive interaction suggests that strain identity and the biotic context of co-infection is important to predict strain dynamics and persistence. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1964-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evelyn C Rynkiewicz
- Ecology, Evolution, and Environmental Biology Department, Columbia University, 1200 Amsterdam Ave, New York, NY, 10027, USA
| | - Julia Brown
- Yale School of Public Health, 60 College St, New Haven, CT, 06510, USA
| | - Danielle M Tufts
- Ecology, Evolution, and Environmental Biology Department, Columbia University, 1200 Amsterdam Ave, New York, NY, 10027, USA
| | - Ching-I Huang
- Ecology, Evolution, and Environmental Biology Department, Columbia University, 1200 Amsterdam Ave, New York, NY, 10027, USA
| | - Helge Kampen
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493, Greifswald, Germany
| | - Stephen J Bent
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Durland Fish
- Yale School of Public Health, 60 College St, New Haven, CT, 06510, USA
| | - Maria A Diuk-Wasser
- Ecology, Evolution, and Environmental Biology Department, Columbia University, 1200 Amsterdam Ave, New York, NY, 10027, USA.
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9
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Buckberry S, Bianco-Miotto T, Bent SJ, Clifton V, Shoubridge C, Shankar K, Roberts CT. Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation. BMC Genomics 2017; 18:10. [PMID: 28049421 PMCID: PMC5209944 DOI: 10.1186/s12864-016-3384-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 03/03/2016] [Accepted: 12/07/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Mammalian development in utero is absolutely dependent on proper placental development, which is ultimately regulated by the placental genome. The regulation of the placental genome can be directly studied by exploring the underlying organisation of the placental transcriptome through a systematic analysis of gene-wise co-expression relationships. RESULTS In this study, we performed a comprehensive analysis of human placental co-expression using RNA sequencing and intergrated multiple transcriptome datasets spanning human gestation. We identified modules of co-expressed genes that are preserved across human gestation, and also identifed modules conserved in the mouse indicating conserved molecular networks involved in placental development and gene expression patterns more specific to late gestation. Analysis of co-expressed gene flanking sequences indicated that conserved co-expression modules in the placenta are regulated by a core set of transcription factors, including ZNF423 and EBF1. Additionally, we identified a gene co-expression module enriched for genes implicated in the pregnancy pathology preeclampsia. By using an independnet transcriptome dataset, we show that these co-expressed genes are differentially expressed in preeclampsia. CONCLUSIONS This study represents a comprehensive characterisation of placental co-expression and provides insight into potential transcriptional regulators that govern conserved molecular programs fundamental to placental development.
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Affiliation(s)
- Sam Buckberry
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.,University of Western Australia, Harry Perkins Institute of Medical Research, Perth, 6009, Australia.,University of Western Australia, Australian Research Council Centre of Excellence in Plant Energy Biology, Perth, 6009, Australia
| | - Tina Bianco-Miotto
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.,The University of Adelaide, School of agriculture, food and wine, Adelaide, 5005, Australia
| | - Stephen J Bent
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia
| | - Vicki Clifton
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia
| | - Cheryl Shoubridge
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia
| | - Kartik Shankar
- University of Arkansas for Medical Sciences, The Department of Pediatrics, Little Rock, 72202, USA
| | - Claire T Roberts
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.
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10
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Jiang D, Tikhomirova A, Bent SJ, Kidd SP. A discrete role for FNR in the transcriptional response to moderate changes in oxygen by Haemophilus influenzae Rd KW20. Res Microbiol 2015; 167:103-13. [PMID: 26499095 DOI: 10.1016/j.resmic.2015.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 07/10/2015] [Revised: 09/21/2015] [Accepted: 09/29/2015] [Indexed: 11/28/2022]
Abstract
The survival by pathogenic bacteria within the specific conditions of an anatomical niche is critical for their persistence. These conditions include the combination of toxic chemicals, such as reactive oxygen (ROS) and reactive nitrogen species (RNS), with factors relevant to cell growth, such as oxygen. Haemophilus influenzae senses oxygen levels largely through the redox state of the intracellular fumarate-nitrate global regulator (FNR). H. influenzae certainly encounters oxygen levels that fluctuate, but in reality, these would rarely reach a state that results in FNR being fully reduced or oxidized. We were therefore interested in the response of H. influenzae to ROS and RNS at moderately high or low oxygen levels and the corresponding role of FNR. At these levels of oxygen, even though the growth rate of an H. influenzae fnr mutant was similar to wild type, its ROS and RNS tolerance was significantly different. Additionally, the subtle changes in oxygen did alter the whole cell transcriptional profile and this was different between the wild type and fnr mutant strains. It was the changed whole cell profile that impacted on ROS/RNS defence, but surprisingly, the FNR-regulated, anaerobic nitrite reductase (NrfA) continued to be expressed and had a role in this phenotype.
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Affiliation(s)
- Donald Jiang
- Research Centre for Infectious Disease, The University of Adelaide, Adelaide, Australia; School of Biological Science, The University of Adelaide, Adelaide, Australia; Agri-Food and Veterinary Authority of Singapore, Singapore.
| | - Alexandra Tikhomirova
- Research Centre for Infectious Disease, The University of Adelaide, Adelaide, Australia; School of Biological Science, The University of Adelaide, Adelaide, Australia.
| | - Stephen J Bent
- School of Biological Science, The University of Adelaide, Adelaide, Australia; Robinson Research Institute, The University of Adelaide, Adelaide, Australia.
| | - Stephen P Kidd
- Research Centre for Infectious Disease, The University of Adelaide, Adelaide, Australia; School of Biological Science, The University of Adelaide, Adelaide, Australia.
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11
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Jungnick S, Margos G, Rieger M, Dzaferovic E, Bent SJ, Overzier E, Silaghi C, Walder G, Wex F, Koloczek J, Sing A, Fingerle V. Borrelia burgdorferi sensu stricto and Borrelia afzelii : Population structure and differential pathogenicity. Int J Med Microbiol 2015; 305:673-81. [DOI: 10.1016/j.ijmm.2015.08.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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12
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Jen FEC, Djoko KY, Bent SJ, Day CJ, McEwan AG, Jennings MP. A genetic screen reveals a periplasmic copper chaperone required for nitrite reductase activity in pathogenicNeisseria. FASEB J 2015; 29:3828-38. [DOI: 10.1096/fj.15-270751] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 05/18/2015] [Indexed: 01/21/2023]
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13
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Carpi G, Walter KS, Bent SJ, Hoen AG, Diuk-Wasser M, Caccone A. Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi. BMC Genomics 2015; 16:434. [PMID: 26048573 PMCID: PMC4458057 DOI: 10.1186/s12864-015-1634-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [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] [Received: 11/11/2014] [Accepted: 05/18/2015] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Rapid and accurate retrieval of whole genome sequences of human pathogens from disease vectors or animal reservoirs will enable fine-resolution studies of pathogen epidemiological and evolutionary dynamics. However, next generation sequencing technologies have not yet been fully harnessed for the study of vector-borne and zoonotic pathogens, due to the difficulty of obtaining high-quality pathogen sequence data directly from field specimens with a high ratio of host to pathogen DNA. RESULTS We addressed this challenge by using custom probes for multiplexed hybrid capture to enrich for and sequence 30 Borrelia burgdorferi genomes from field samples of its arthropod vector. Hybrid capture enabled sequencing of nearly the complete genome (~99.5 %) of the Borrelia burgdorferi pathogen with 132-fold coverage, and identification of up to 12,291 single nucleotide polymorphisms per genome. CONCLUSIONS The proprosed culture-independent method enables efficient whole genome capture and sequencing of pathogens directly from arthropod vectors, thus making population genomic study of vector-borne and zoonotic infectious diseases economically feasible and scalable. Furthermore, given the similarities of invertebrate field specimens to other mixed DNA templates characterized by a high ratio of host to pathogen DNA, we discuss the potential applicabilty of hybrid capture for genomic study across diverse study systems.
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Affiliation(s)
- Giovanna Carpi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA.
| | - Katharine S Walter
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA.
| | - Stephen J Bent
- Robinson Research Institute, University of Adelaide, 5005, Adelaide, SA, Australia.
| | - Anne Gatewood Hoen
- The Geisel School of Medicine, Dartmouth College, 03755, Hanover, NH, USA.
| | - Maria Diuk-Wasser
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA. .,Department of Ecology, Evolution and Environmental Biology, Columbia University, 10027, New York, NY, USA.
| | - Adalgisa Caccone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA. .,Department of Ecology and Evolutionary Biology, Yale University, 06520, New Haven, CT, USA.
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14
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Bersten DC, Sullivan AE, Li D, Bhakti V, Bent SJ, Whitelaw ML. Inducible and reversible lentiviral and Recombination Mediated Cassette Exchange (RMCE) systems for controlling gene expression. PLoS One 2015; 10:e0116373. [PMID: 25768837 PMCID: PMC4358958 DOI: 10.1371/journal.pone.0116373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 12/08/2014] [Indexed: 11/19/2022] Open
Abstract
Manipulation of gene expression to invoke loss of function (LoF) or gain of function (GoF) phenotypes is important for interrogating complex biological questions both in vitro and in vivo. Doxycycline (Dox)-inducible gene expression systems are commonly used although success is often limited by high background and insufficient sensitivity to Dox. Here we develop broadly applicable platforms for reliable, tightly controlled and reversible Dox-inducible systems for lentiviral mediated generation of cell lines or FLP Recombination-Mediated Cassette Exchange (RMCE) into the Collagen 1a1 (Col1a1) locus (FLP-In Col1a1) in mouse embryonic stem cells. We significantly improve the flexibility, usefulness and robustness of the Dox-inducible system by using Tetracycline (Tet) activator (Tet-On) variants which are more sensitive to Dox, have no background activity and are expressed from single Gateway-compatible constructs. We demonstrate the usefulness of these platforms in ectopic gene expression or gene knockdown in multiple cell lines, primary neurons and in FLP-In Col1a1 mouse embryonic stem cells. We also improve the flexibility of RMCE Dox-inducible systems by generating constructs that allow for tissue or cell type-specific Dox-inducible expression and generate a shRNA selection algorithm that can effectively predict potent shRNA sequences able to knockdown gene expression from single integrant constructs. These platforms provide flexible, reliable and broadly applicable inducible expression systems for studying gene function.
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Affiliation(s)
- David C. Bersten
- School of Molecular and Biomedical Science (Biochemistry), The University of Adelaide, Adelaide, South Australia, Australia
- Institute of Molecular Pathology, The University of Adelaide, Adelaide, South Australia, Australia
- * E-mail: (MLW); (DCB)
| | - Adrienne E. Sullivan
- School of Molecular and Biomedical Science (Biochemistry), The University of Adelaide, Adelaide, South Australia, Australia
- Institute of Molecular Pathology, The University of Adelaide, Adelaide, South Australia, Australia
| | - Dian Li
- School of Molecular and Biomedical Science (Biochemistry), The University of Adelaide, Adelaide, South Australia, Australia
- Institute of Molecular Pathology, The University of Adelaide, Adelaide, South Australia, Australia
| | - Veronica Bhakti
- School of Molecular and Biomedical Science (Biochemistry), The University of Adelaide, Adelaide, South Australia, Australia
- Institute of Molecular Pathology, The University of Adelaide, Adelaide, South Australia, Australia
| | - Stephen J. Bent
- School of Molecular and Biomedical Science (Genetics), The University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Murray L. Whitelaw
- School of Molecular and Biomedical Science (Biochemistry), The University of Adelaide, Adelaide, South Australia, Australia
- Institute of Molecular Pathology, The University of Adelaide, Adelaide, South Australia, Australia
- * E-mail: (MLW); (DCB)
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15
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Aloia AL, Eyre NS, Black S, Bent SJ, Gaeguta A, Guo Z, Narayana SK, Chase R, Locarnini S, Carr JM, Howe JA, Beard MR. Generation of a chimeric hepatitis C replicon encoding a genotype-6a NS3 protease and assessment of boceprevir (SCH503034) sensitivity and drug-associated mutations. Antivir Ther 2014; 20:271-80. [PMID: 25222708 DOI: 10.3851/imp2850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2014] [Indexed: 02/07/2023]
Abstract
BACKGROUND Genotype (gt)6 HCV is common amongst HCV-positive populations of the Asia-Pacific region but cell culture models for this gt have only recently been developed. Boceprevir (SCH503034) is a clinically available inhibitor of the HCV NS3 protein. We investigated the efficacy of boceprevir for inhibiting replication of a chimeric gt1b replicon encoding a gt6a NS3 protease and defined the development of mutations in the protease when boceprevir treatment was applied. METHODS We constructed a chimeric gt1b subgenomic replicon encoding a gt6 NS3 protease (NS3p) sequence (gt6NS3p_gt1b). The boceprevir EC50 value against replication of this replicon was determined using quantitative reverse transcriptase PCR. Next-generation sequencing was used to identify nucleotide changes associated with boceprevir resistance. The replication capacities of chimeric replicons containing mutations associated with boceprevir resistance were determined by colony formation efficiency assays. RESULTS The boceprevir EC50 value for the gt6NS3p_gt1b replicon was 535 ±79 nM. Boceprevir-resistant gt6NS3p_gt1b replicon cell lines could be selected and they demonstrated drug-associated amino acid changes that have previously been reported in other HCV gts. Interestingly, no mutations were observed at A156, a position defined for boceprevir resistance in gt1 NS3p, while mutation at N122, which is rarely reported in boceprevir-resistant gt1 proteases, was frequently observed. Re-introduction of these mutations into the chimeric replicon altered their replication capacity, ranging from complete abolishment of replication (A156T) to increasing replication capacity (V36A, N122S). This report provides the first characterization of gt6 HCV resistance to boceprevir. CONCLUSIONS A chimeric HCV replicon encoding gt6 NS3 protease is sensitive to boceprevir and develops drug-resistant mutations at amino acid sites previously reported for other gts. Mutation at N122 also appears to be associated with boceprevir resistance in the gt6 NS3 protease.
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Affiliation(s)
- Amanda L Aloia
- School of Molecular and Biomedical Science, Adelaide, The University of Adelaide and Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
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16
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Diuk-Wasser MA, Liu Y, Steeves TK, Folsom-O'Keefe C, Dardick KR, Lepore T, Bent SJ, Usmani-Brown S, Telford SR, Fish D, Krause PJ. Monitoring human babesiosis emergence through vector surveillance New England, USA. Emerg Infect Dis 2014; 20:225-31. [PMID: 24447577 PMCID: PMC3901474 DOI: 10.3201/eid2002.130644] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human babesiosis is an emerging tick-borne disease caused by the intraerythrocytic protozoan Babesia microti. Its geographic distribution is more limited than that of Lyme disease, despite sharing the same tick vector and reservoir hosts. The geographic range of babesiosis is expanding, but knowledge of its range is incomplete and relies exclusively on reports of human cases. We evaluated the utility of tick-based surveillance for monitoring disease expansion by comparing the ratios of the 2 infections in humans and ticks in areas with varying B. microti endemicity. We found a close association between human disease and tick infection ratios in long-established babesiosis-endemic areas but a lower than expected incidence of human babesiosis on the basis of tick infection rates in new disease-endemic areas. This finding suggests that babesiosis at emerging sites is underreported. Vector-based surveillance can provide an early warning system for the emergence of human babesiosis.
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17
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Buckberry S, Bianco-Miotto T, Bent SJ, Dekker GA, Roberts CT. Integrative transcriptome meta-analysis reveals widespread sex-biased gene expression at the human fetal-maternal interface. Mol Hum Reprod 2014; 20:810-9. [PMID: 24867328 PMCID: PMC4106635 DOI: 10.1093/molehr/gau035] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [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: 03/13/2014] [Revised: 04/23/2014] [Accepted: 05/01/2014] [Indexed: 12/16/2022] Open
Abstract
As males and females share highly similar genomes, the regulation of many sexually dimorphic traits is constrained to occur through sex-biased gene regulation. There is strong evidence that human males and females differ in terms of growth and development in utero and that these divergent growth strategies appear to place males at increased risk when in sub-optimal conditions. Since the placenta is the interface of maternal-fetal exchange throughout pregnancy, these developmental differences are most likely orchestrated by differential placental function. To date, progress in this field has been hampered by a lack of genome-wide information on sex differences in placental gene expression. Therefore, our motivation in this study was to characterize sex-biased gene expression in the human placenta. We obtained gene expression data for >300 non-pathological placenta samples from 11 microarray datasets and applied mapping-based array probe re-annotation and inverse-variance meta-analysis methods which showed that >140 genes (false discovery rate (FDR) <0.05) are differentially expressed between male and female placentae. A majority of these genes (>60%) are autosomal, many of which are involved in high-level regulatory processes such as gene transcription, cell growth and proliferation and hormonal function. Of particular interest, we detected higher female expression from all seven genes in the LHB-CGB cluster, which includes genes involved in placental development, the maintenance of pregnancy and maternal immune tolerance of the conceptus. These results demonstrate that sex-biased gene expression in the normal human placenta occurs across the genome and includes genes that are central to growth, development and the maintenance of pregnancy.
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Affiliation(s)
- Sam Buckberry
- The Robinson Research Institute, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide 5005, Australia
| | - Tina Bianco-Miotto
- The Robinson Research Institute, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide 5005, Australia School of Agriculture Food & Wine, The University of Adelaide, Adelaide 5005, Australia
| | - Stephen J Bent
- The Robinson Research Institute, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide 5005, Australia
| | - Gustaaf A Dekker
- The Robinson Research Institute, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide 5005, Australia Lyell McEwin Hospital, Elizabeth Vale, SA 5112, Australia
| | - Claire T Roberts
- The Robinson Research Institute, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide 5005, Australia
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18
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Sarker S, Ghorashi SA, Forwood JK, Bent SJ, Peters A, Raidal SR. Phylogeny of beak and feather disease virus in cockatoos demonstrates host generalism and multiple-variant infections within Psittaciformes. Virology 2014; 460-461:72-82. [PMID: 25010272 DOI: 10.1016/j.virol.2014.04.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [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: 12/05/2013] [Revised: 01/09/2014] [Accepted: 04/17/2014] [Indexed: 01/18/2023]
Abstract
Phylogenetic analyses of the highly genetically diverse but antigenically conserved, single-stranded circular, DNA genome of the avian circovirus, beak and feather disease virus (BFDV) from cockatoo species throughout Australia demonstrated a high mutation rate for BFDV (orders of magnitude fall in the range of 10(-4) substitutions/site/year) along with strong support for recombination indicating active cross-species transmission in various subpopulations. Multiple variants of BFDV were demonstrated with at least 30 genotypic variants identified within nine individual birds, with one containing up to 7 variants. Single genetic variants were detected in feathers from 2 birds but splenic tissue provided further variants. The rich BFDV genetic diversity points to Australasia as the most likely geographical origin of this virus and supports flexible host switching. We propose this as evidence of Order-wide host generalism in the Psittaciformes characterised by high mutability that is buffered by frequent recombination and slow replication strategy.
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Affiliation(s)
- Subir Sarker
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia; Graham Centre for Agricultural Innovation, NSW Department of Primary Industries and Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia.
| | - Seyed A Ghorashi
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia; Graham Centre for Agricultural Innovation, NSW Department of Primary Industries and Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia.
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia; Graham Centre for Agricultural Innovation, NSW Department of Primary Industries and Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia.
| | - Stephen J Bent
- Molecular and Biomedical Science, Faculty of Sciences, The University of Adelaide, Australia.
| | - Andrew Peters
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia; Graham Centre for Agricultural Innovation, NSW Department of Primary Industries and Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia.
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia; Graham Centre for Agricultural Innovation, NSW Department of Primary Industries and Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia.
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Abstract
Summary: High-throughput gene expression microarrays are currently the most efficient method for transcriptome-wide expression analyses. Consequently, gene expression data available through public repositories have largely been obtained from microarray experiments. However, the metadata associated with many publicly available expression microarray datasets often lacks sample sex information, therefore limiting the reuse of these data in new analyses or larger meta-analyses where the effect of sex is to be considered. Here, we present the massiR package, which provides a method for researchers to predict the sex of samples in microarray datasets. Using information from microarray probes representing Y chromosome genes, this package implements unsupervised clustering methods to classify samples into male and female groups, providing an efficient way to identify or confirm the sex of samples in mammalian microarray datasets. Availability and implementation:massiR is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at bioconductor.org and are provided under a GPL-2 license. Contact:sam.buckberry@adelaide.edu.au Supplementary information:Supplementary data are available at Bioinformatics online
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Affiliation(s)
- Sam Buckberry
- The Robinson Research Institute, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide 5005, Australia and School of Agriculture Food and Wine, The University of Adelaide, Adelaide 5005, Australia
| | - Stephen J Bent
- The Robinson Research Institute, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide 5005, Australia and School of Agriculture Food and Wine, The University of Adelaide, Adelaide 5005, Australia
| | - Tina Bianco-Miotto
- The Robinson Research Institute, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide 5005, Australia and School of Agriculture Food and Wine, The University of Adelaide, Adelaide 5005, AustraliaThe Robinson Research Institute, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide 5005, Australia and School of Agriculture Food and Wine, The University of Adelaide, Adelaide 5005, Australia
| | - Claire T Roberts
- The Robinson Research Institute, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide 5005, Australia and School of Agriculture Food and Wine, The University of Adelaide, Adelaide 5005, Australia
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20
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Ishak N, Tikhomirova A, Bent SJ, Ehrlich GD, Hu FZ, Kidd SP. There is a specific response to pH by isolates of Haemophilus influenzae and this has a direct influence on biofilm formation. BMC Microbiol 2014; 14:47. [PMID: 24555828 PMCID: PMC3938079 DOI: 10.1186/1471-2180-14-47] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [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] [Received: 12/09/2013] [Accepted: 02/19/2014] [Indexed: 12/22/2022] Open
Abstract
Background Haemophilus influenzae colonizes the nasopharynx as a commensal. Strain-specific factors allow some strains to migrate to particular anatomical niches, such as the middle ear, bronchi or blood, and induce disease by surviving within the conditions present at these sites in the body. It is established that H. influenzae colonization and in some cases survival is highly dependent on their ability to form a biofilm. Biofilm formation is a key trait in the development of chronic infection by certain isolates. This is exemplified by the contrast between the biofilm-forming strains found in middle ear infections and those isolates that survive within the blood and are rarely associated with biofilm development. Results Screening a group of H. influenzae strains revealed only slight variations in their growth across a range of pH conditions. However, some isolates responded to a pH of 8.0 by the formation of a biofilm. While the type b capsular blood isolate Eagan did not form a biofilm and grew at the same rate regardless of pH 6.8-8.0, transcriptomic analyses demonstrated that at pH 8.0 it uniquely induced a gluconate-uptake and metabolism pathway, which concurrently imports H+. A non-typeable H. influenzae, isolated from the middle ear, induced biofilm formation at pH 8.0, and at this pH it induced a series of iron acquisition genes, consistent with previous studies linking iron homeostasis to biofilm lifestyle. Conclusions Different strains of H. influenzae cope with changes in environmental factors using strain-specific mechanisms. These pathways define the scope and mode of niche-survival for an isolate. The pH is a property that is different from the middle ear (at least pH 8.0) compared to other sites that H. influenzae can colonize and infect. The transcriptional response to increasing pH by H. influenzae varies between strains, and pH is linked to pathways that allow strains to either continue free-living growth or induction of a biofilm. We showed that a biofilm-forming isolate induced iron metabolism pathways, whereas a strain that does not form biofilm at increasing pH induced mechanisms for growth and pH homeostasis based on sugar acid transport.
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Affiliation(s)
| | | | | | | | | | - Stephen P Kidd
- Research Centre for Infectious Diseases, The University of Adelaide, North Terrace Campus, Adelaide, South Australia 5005, Australia.
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21
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Diuk-Wasser MA, Liu Y, Steeves TK, Folsom-O’Keefe C, Dardick KR, Lepore T, Bent SJ, Usmani-Brown S, Telford SR, Fish D, Krause PJ. Monitoring Human Babesiosis Emergence through Vector Surveillance New England, USA. Emerg Infect Dis 2014. [DOI: 10.3201/eid1302/130644] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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22
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Rollend L, Bent SJ, Krause PJ, Usmani-Brown S, Steeves TK, States SL, Lepore T, Ryan R, Dias F, Ben Mamoun C, Fish D, Diuk-Wasser MA. Quantitative PCR for detection of Babesia microti in Ixodes scapularis ticks and in human blood. Vector Borne Zoonotic Dis 2013; 13:784-90. [PMID: 24107203 DOI: 10.1089/vbz.2011.0935] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Babesia microti, the primary cause of human babesiosis in the United States, is transmitted by Ixodes scapularis ticks; transmission may also occur through blood transfusion and transplacentally. Most infected people experience a viral-like illness that resolves without complication, but those who are immunocompromised may develop a serious and prolonged illness that is sometimes fatal. The geographic expansion and increasing incidence of human babesiosis in the northeastern and midwestern United States highlight the need for high-throughput sensitive and specific assays to detect parasites in both ticks and humans with the goals of improving epidemiological surveillance, diagnosis of acute infections, and screening of the blood supply. Accordingly, we developed a B. microti-specific quantitative PCR (qPCR) assay (named BabMq18) designed to detect B. microti DNA in tick and human blood samples using a primer and probe combination that targets the 18S rRNA gene of B. microti. This qPCR assay was compared with two nonquantitative B. microti PCR assays by testing tick samples and was found to exhibit higher sensitivity for detection of B. microti DNA. The BabMq18 assay has a detection threshold of 10 copies per reaction and does not amplify DNA in I. scapularis ticks infected with Babesia odocoilei, Borrelia burgdorferi, Borrelia miyamotoi, or Anaplasma phagocytophilum. This highly sensitive and specific qPCR assay can be used for detection of B. microti DNA in both tick and human samples. Finally, we report the prevalence of B. microti infection in field-collected I. scapularis nymphs from three locations in southern New England that present disparate incidences of human babesiosis.
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Affiliation(s)
- Lindsay Rollend
- 1 Department of Epidemiology and Public Health, Yale School of Public Health , New Haven, Connecticut
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23
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Brinkerhoff RJ, Folsom-O'Keefe CM, Streby HM, Bent SJ, Tsao K, Diuk-Wasser MA. Regional variation in immature Ixodes scapularis parasitism on North American songbirds: implications for transmission of the Lyme pathogen, Borrelia burgdorferi. J Med Entomol 2011; 48:422-428. [PMID: 21485384 DOI: 10.1603/me10060] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Borrelia burgdorferi, the etiological agent of Lyme disease, is transmitted among hosts by the black-legged tick, Ixodes scapularis, a species that regularly parasitizes various vertebrate hosts, including birds, in its immature stages. Lyme disease risk in the United States is highest in the Northeast and in the upper Midwest where I. scapularis ticks are most abundant. Because birds might be important to the range expansion of I. scapularis and B. burgdorferi, we explored spatial variation in patterns of I. scapularis parasitism on songbirds, as well as B. burgdorferi infection in bird-derived I. scapularis larvae. We sampled birds at 23 sites in the eastern United States to describe seasonal patterns of I. scapularis occurrence on birds, and we screened a subset of I. scapularis larvae for presence of B. burgdorferi. Timing of immature I. scapularis occurrence on birds is consistent with regional variation in host-seeking activity with a generally earlier peak in larval parasitism on birds in the Midwest. Significantly more I. scapularis larvae occurred on birds that were contemporaneously parasitized by nymphs in the Midwest than the Northeast, and the proportion of birds that yielded B. burgdorferi-infected larvae was also higher in the Midwest. We conclude that regional variation in immature I. scapularis phenology results in different temporal patterns of parasitism on birds, potentially resulting in differential importance of birds to B. burgdorferi transmission dynamics among regions.
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Affiliation(s)
- R Jory Brinkerhoff
- Yale School of Public Health, 60 College Street, New Haven, CT 06520-8034, USA.
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24
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Brinkerhoff RJ, Bent SJ, Folsom-O'Keefe CM, Tsao K, Hoen AG, Barbour AG, Diuk-Wasser MA. Genotypic diversity of Borrelia burgdorferi strains detected in Ixodes scapularis larvae collected from North American songbirds. Appl Environ Microbiol 2010; 76:8265-8. [PMID: 20971869 PMCID: PMC3008240 DOI: 10.1128/aem.01585-10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Accepted: 10/11/2010] [Indexed: 11/20/2022] Open
Abstract
We genotyped Borrelia burgdorferi strains detected in larvae of Ixodes scapularis removed from songbirds and compared them with those found in host-seeking I. scapularis nymphs sampled throughout the eastern United States. Birds are capable of transmitting most known genotypes, albeit at different frequencies than expected based on genotypes found among host-seeking nymphs.
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Affiliation(s)
- R Jory Brinkerhoff
- Division of Epidemiology of Microbial Diseases, Yale School of Public Health, Box 208034, 60 College St., New Haven, Connecticut 06520-8034, USA.
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25
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Davis S, Bent SJ. Loop analysis for pathogens: niche partitioning in the transmission graph for pathogens of the North American tick Ixodes scapularis. J Theor Biol 2010; 269:96-103. [PMID: 20950628 DOI: 10.1016/j.jtbi.2010.10.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 10/07/2010] [Accepted: 10/07/2010] [Indexed: 10/19/2022]
Abstract
In population biology, loop analysis is a method of decomposing a life cycle graph into life history pathways so as to compare the relative contributions of pathways to the population growth rate across species and populations. We apply loop analysis to the transmission graph of five pathogens known to infect the black-legged tick, Ixodes scapularis. In this context loops represent repeating chains of transmission that could maintain the pathogen. They hence represent completions of the life cycle, in much the same way as loops in a life cycle graph do for plants and animals. The loop analysis suggests the five pathogens fall into two distinct groups. Borellia burgdorferi, Babesia microti and Anaplasma phagocytophilum rely almost exclusively on a single loop representing transmission to susceptible larvae feeding on vertebrate hosts that were infected by nymphs. Borellia miyamotoi, in contrast, circulates among a separate set of host types and utilizes loops that are a mix of vertical transmission and horizontal transmission. For B. miyamotoi the main loop is from vertebrate hosts to susceptible nymphs, where the vertebrate hosts were infected by larvae that were infected from birth. The results for Powassan virus are similar to B. miyamotoi. The predicted impacts of the known variation in tick phenology between populations of I. scapularis in the Midwest and Northeast of the United States are hence markedly different for the two groups. All of these pathogens benefit, though, from synchronous activity of larvae and nymphs.
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Affiliation(s)
- Stephen Davis
- Yale School of Public Health, 60 College St., P.O. Box 208034, New Haven, CT 06520, USA.
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Pérez de León AA, Strickman DA, Knowles DP, Fish D, Thacker E, de la Fuente J, Krause PJ, Wikel SK, Miller RS, Wagner GG, Almazán C, Hillman R, Messenger MT, Ugstad PO, Duhaime RA, Teel PD, Ortega-Santos A, Hewitt DG, Bowers EJ, Bent SJ, Cochran MH, McElwain TF, Scoles GA, Suarez CE, Davey R, Howell Freeman JM, Lohmeyer K, Li AY, Guerrero FD, Kammlah DM, Phillips P, Pound JM. One Health approach to identify research needs in bovine and human babesioses: workshop report. Parasit Vectors 2010; 3:36. [PMID: 20377902 PMCID: PMC2859369 DOI: 10.1186/1756-3305-3-36] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [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] [Received: 02/06/2010] [Accepted: 04/08/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Babesia are emerging health threats to humans and animals in the United States. A collaborative effort of multiple disciplines to attain optimal health for people, animals and our environment, otherwise known as the One Health concept, was taken during a research workshop held in April 2009 to identify gaps in scientific knowledge regarding babesioses. The impetus for this analysis was the increased risk for outbreaks of bovine babesiosis, also known as Texas cattle fever, associated with the re-infestation of the U.S. by cattle fever ticks. RESULTS The involvement of wildlife in the ecology of cattle fever ticks jeopardizes the ability of state and federal agencies to keep the national herd free of Texas cattle fever. Similarly, there has been a progressive increase in the number of cases of human babesiosis over the past 25 years due to an increase in the white-tailed deer population. Human babesiosis due to cattle-associated Babesia divergens and Babesia divergens-like organisms have begun to appear in residents of the United States. Research needs for human and bovine babesioses were identified and are presented herein. CONCLUSIONS The translation of this research is expected to provide veterinary and public health systems with the tools to mitigate the impact of bovine and human babesioses. However, economic, political, and social commitments are urgently required, including increased national funding for animal and human Babesia research, to prevent the re-establishment of cattle fever ticks and the increasing problem of human babesiosis in the United States.
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Abstract
Succession is defined as changes in biological communities over time. It has been extensively studied in plant communities, but little is known about bacterial succession, in particular in environments such as High Arctic glacier forelands. Bacteria carry out key processes in the development of soil, biogeochemical cycling and facilitating plant colonization. In this study we sampled two roughly parallel chronosequences in the foreland of Midre Lovén glacier on Svalbard, Norway and tested whether any of several factors were associated with changes in the structure of bacterial communities, including time after glacier retreat, horizontal variation caused by the distance between chronosequences and vertical variation at two soil depths. The structures of soil bacterial communities at different locations were compared using terminal restriction fragment length polymorphisms of 16S rRNA genes, and the data were analyzed by sequential analysis of log-linear statistical models. Although no significant differences in community structure were detected between the two chronosequences, statistically significant differences between sampling locations in the surface and mineral soils could be demonstrated even though glacier forelands are patchy and dynamic environments. These findings suggest that bacterial succession occurs in High Arctic glacier forelands but may differ in different soil depths.
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Affiliation(s)
- Ursel M.E. Schütte
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844
- Initiative for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, 83844
- Department of Biology, University of Tromsø, 9037 Tromsø, Norway
| | - Zaid Abdo
- Department of Mathematics, University of Idaho, Moscow, ID, 83844
- Department of Statistics, University of Idaho, Moscow, ID, 83844
- Initiative for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, 83844
| | - Stephen J. Bent
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844
- Initiative for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, 83844
| | - Christopher J. Williams
- Department of Statistics, University of Idaho, Moscow, ID, 83844
- Initiative for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, 83844
| | - G. Maria Schneider
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844
| | - Bjørn Solheim
- Department of Biology, University of Tromsø, 9037 Tromsø, Norway
| | - Larry J. Forney
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844
- Initiative for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, 83844
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Hoen AG, Margos G, Bent SJ, Diuk-Wasser MA, Barbour A, Kurtenbach K, Fish D. Phylogeography of Borrelia burgdorferi in the eastern United States reflects multiple independent Lyme disease emergence events. Proc Natl Acad Sci U S A 2009; 106:15013-8. [PMID: 19706476 PMCID: PMC2727481 DOI: 10.1073/pnas.0903810106] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [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: 04/22/2009] [Indexed: 11/18/2022] Open
Abstract
Since its first description in coastal Connecticut in 1976, both the incidence of Lyme disease and the geographic extent of endemic areas in the US have increased dramatically. The rapid expansion of Lyme disease into its current distribution in the eastern half of the US has been due to the range expansion of the tick vector, Ixodes scapularis, upon which the causative agent, Borrelia burgdorferi is dependent for transmission to humans. In this study, we examined the phylogeographic population structure of B. burgdorferi throughout the range of I. scapularis-borne Lyme disease using multilocus sequence typing based on bacterial housekeeping genes. We show that B. burgdorferi populations from the Northeast and Midwest are genetically distinct, but phylogenetically related. Our findings provide strong evidence of prehistoric population size expansion and east-to-west radiation of descendent clones from founding sequence types in the Northeast. Estimates of the time scale of divergence of northeastern and midwestern populations suggest that B. burgdorferi was present in these regions of North America many thousands of years before European settlements. We conclude that B. burgdorferi populations have recently reemerged independently out of separate relict foci, where they have persisted since precolonial times.
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Affiliation(s)
- Anne Gatewood Hoen
- Department of Epidemiology and Public Health, Yale School of Medicine, New Haven, CT 06520
| | - Gabriele Margos
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom; and
| | - Stephen J. Bent
- Department of Epidemiology and Public Health, Yale School of Medicine, New Haven, CT 06520
| | - Maria A. Diuk-Wasser
- Department of Epidemiology and Public Health, Yale School of Medicine, New Haven, CT 06520
| | - Alan Barbour
- Departments of Microbiology and Molecular Genetics and Medicine and Pacific-Southwest Center of Excellence, University of California, Irvine, CA 92697
| | - Klaus Kurtenbach
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom; and
| | - Durland Fish
- Department of Epidemiology and Public Health, Yale School of Medicine, New Haven, CT 06520
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Bent SJ, Forney LJ. The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. ISME J 2008; 2:689-95. [DOI: 10.1038/ismej.2008.44] [Citation(s) in RCA: 214] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Bent SJ, Pierson JD, Forney LJ. Measuring species richness based on microbial community fingerprints: the emperor has no clothes. Appl Environ Microbiol 2007; 73:2399-401; author reply 2399-401. [PMID: 17403942 PMCID: PMC1855686 DOI: 10.1128/aem.02383-06] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Stephen J. Bent
- Department of Biological SciencesUniversity of IdahoMoscow, Idaho 83844
| | - Jacob D. Pierson
- Department of Biological SciencesUniversity of IdahoMoscow, Idaho 83844
| | - Larry J. Forney
- Department of Biological SciencesUniversity of IdahoMoscow, Idaho 83844
- Phone: 208 885 6280, Fax: 208 885 7905, E-mail:
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Shyu C, Soule T, Bent SJ, Foster JA, Forney LJ. MiCA: a web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes. Microb Ecol 2007; 53:562-70. [PMID: 17406775 DOI: 10.1007/s00248-006-9106-0] [Citation(s) in RCA: 144] [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] [Subscribe] [Scholar Register] [Received: 05/15/2005] [Accepted: 05/18/2005] [Indexed: 05/12/2023]
Abstract
A web-based resource, Microbial Community Analysis (MiCA), has been developed to facilitate studies on microbial community ecology that use analyses of terminal-restriction fragment length polymorphisms (T-RFLP) of 16S and 18S rRNA genes. MiCA provides an intuitive web interface to access two specialized programs and a specially formatted database of 16S ribosomal RNA sequences. The first program performs virtual polymerase chain reaction (PCR) amplification of rRNA genes and restriction of the amplicons using primer sequences and restriction enzymes chosen by the user. This program, in silico PCR and Restriction (ISPaR), uses a binary encoding of DNA sequences to rapidly scan large numbers of sequences in databases searching for primer annealing and restriction sites while permitting the user to specify the number of mismatches in primer sequences. ISPaR supports multiple digests with up to three enzymes. The number of base pairs between the 5' and 3' primers and the proximal restriction sites can be reported, printed, or exported in various formats. The second program, APLAUS, infers a plausible community structure(s) based on T-RFLP data supplied by a user. APLAUS estimates the relative abundances of populations and reports a listing of phylotypes that are consistent with the empirical data. MiCA is accessible at http://mica.ibest.uidaho.edu/.
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Affiliation(s)
- Conrad Shyu
- Department of Computer Science, University of Idaho, Moscow, ID 83844, USA
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Abdo Z, Schüette UME, Bent SJ, Williams CJ, Forney LJ, Joyce P. Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environ Microbiol 2006; 8:929-38. [PMID: 16623749 DOI: 10.1111/j.1462-2920.2005.00959.x] [Citation(s) in RCA: 349] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The analysis of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes has proven to be a facile means to compare microbial communities and presumptively identify abundant members. The method provides data that can be used to compare different communities based on similarity or distance measures. Once communities have been clustered into groups, clone libraries can be prepared from sample(s) that are representative of each group in order to determine the phylogeny of the numerically abundant populations in a community. In this paper methods are introduced for the statistical analysis of T-RFLP data that include objective methods for (i) determining a baseline so that 'true' peaks in electropherograms can be identified; (ii) a means to compare electropherograms and bin fragments of similar size; (iii) clustering algorithms that can be used to identify communities that are similar to one another; and (iv) a means to select samples that are representative of a cluster that can be used to construct 16S rRNA gene clone libraries. The methods for data analysis were tested using simulated data with assumptions and parameters that corresponded to actual data. The simulation results demonstrated the usefulness of these methods in their ability to recover the true microbial community structure generated under the assumptions made. Software for implementing these methods is available at http://www.ibest.uidaho.edu/tools/trflp_stats/index.php.
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Affiliation(s)
- Zaid Abdo
- Department of Mathematics, University of Idaho, Moscow, ID 83844-1104, USA.
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Zhou X, Bent SJ, Schneider MG, Davis CC, Islam MR, Forney LJ. Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods. Microbiology (Reading) 2004; 150:2565-2573. [PMID: 15289553 DOI: 10.1099/mic.0.26905-0] [Citation(s) in RCA: 310] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The normal microbial flora of the vagina plays an important role in preventing genital and urinary tract infections in women. Thus an accurate understanding of the composition and ecology of the ecosystem is important to understanding the aetiology of these diseases. Common wisdom is that lactobacilli dominate the normal vaginal microflora of post-pubertal women. However, this conclusion is based on methods that require cultivation of microbial populations; an approach that is known to yield a biased and incomplete assessment of microbial community structure. In this study cultivation-independent methods were used to analyse samples collected from the mid-vagina of five normal healthy Caucasian women between the ages of 28 and 44. Total microbial community DNA was isolated following resuspension of microbial cells from vaginal swabs. To identify the constituent numerically dominant populations in each community 16S rRNA gene libraries were prepared following PCR amplification using the 8f and 926r primers. From each library, the DNA sequences of approximately 200 16S rRNA clones were determined and subjected to phylogenetic analyses. The diversity and kinds of organisms that comprise the vaginal microbial community varied among women. Species of Lactobacillus appeared to dominate the communities in four of the five women. However, the community of one woman was dominated by Atopobium sp., whereas a second woman had appreciable numbers of Megasphaera sp., Atopobium sp. and Leptotrichia sp., none of which have previously been shown to be common members of the vaginal ecosystem. Of the women whose communities were dominated by lactobacilli, there were two distinct clusters, each of which consisted of a single species. One class consisted of two women with genetically divergent clones that were related to Lactobacillus crispatus, whereas the second group of two women had clones of Lactobacillus iners that were highly related to a single phylotype. These surprising results suggest that culture-independent methods can provide new insights into the diversity of bacterial species found in the human vagina, and this information could prove to be pivotal in understanding risk factors for various infectious diseases.
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Affiliation(s)
- Xia Zhou
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Stephen J Bent
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Maria G Schneider
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | | | - Mohammed R Islam
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Larry J Forney
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
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Abstract
The number, spatial distribution, and significance of genetically distinguishable ecotypes of prokaryotes in the environment are poorly understood. Oda et al. (Y. Oda, B. Star, L. A. Huisman, J. C. Gottschal, and L. J. Forney, Appl. Environ. Microbiol. 69:xxx-xxx, 2003) have shown that Rhodopseudomonas palustris ecotypes were lognormally distributed along a 10-m transect and that multiple strains of the species could coexist in 0.5-g sediment samples. To extend these observations, we investigated the clonal diversity of R. palustris in 0.5-g samples taken from the corners and center of a 1-m square. A total of 35 or 36 clones were recovered by direct plating from each sample and were characterized by BOX A1R repetitive element-PCR genomic DNA fingerprinting. Isolates with fingerprint images that were >/=80% similar to each other were defined as the same genotype. Among the 178 isolates studied, 32 genotypes were identified, and each genotype contained between 1 and 40 isolates. These clusters were consistent with minor variations found in 16S rRNA gene sequences. The Shannon indices of the genotypic diversity within each location ranged from 1.08 (5 genotypes) to 2.18 (13 genotypes). Comparison of the rank abundance of genotypes found in pairs of locations showed that strains from three locations were similar to each other, with Morisita-Horn similarity coefficients ranging from 0.59 to 0.71. All comparisons involving the remaining two locations resulted in coefficients between 0 and 0.12. From these results we inferred that the patterns of ecotype diversity at the sampling site are patchy at a 1-m scale and postulated that factors such as mixing, competitive interactions, and microhabitat variability are likely to be responsible for the maintenance of the similarities between some locations and the differences between others.
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Affiliation(s)
- S J Bent
- University of Idaho, Moscow, Idaho, USA
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Semevolos SA, Brower-Toland BD, Bent SJ, Nixon AJ. Parathyroid hormone-related peptide and indian hedgehog expression patterns in naturally acquired equine osteochondrosis. J Orthop Res 2002; 20:1290-7. [PMID: 12472242 DOI: 10.1016/s0736-0266(02)00055-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Early changes in parathyroid hormone-related peptide (PTH-rP) and Indian hedgehog (Ihh) expression were examined in equine articular osteochondrosis (OC) as a model of a naturally acquired dyschondroplasia. Cartilage was harvested from OC-affected femoropatellar or scapulohumeral joints from immature horses and normal control horses of similar age. PTH-rP expression levels were assessed by semi-quantitative PCR, in situ hybridization, and immunohistochemistry. Ihh protein expression levels were assessed by immunohistochemistry. Elevated PTH-rP protein and mRNA expression were identified in the deeper layers of affected articular cartilage and the fibrous tissue of interposing clefts. These changes were confined to the chondrocytes in the OC-affected cartilage, which had significantly increased PTH-rP protein and mRNA expression when compared to control cartilages. Ihh protein expression showed similar distribution as PTH-rP in the deeper layers of articular cartilage; however, only a trend for increased Ihh immunostaining was evident in the OC cartilage when compared to the normal cartilage. Increased PTH-rP expression in prehypertrophic chondrocytes of diseased OC cartilage suggests a possible link between this peptide and the delayed ossification, which is a consistent histologic alteration in OC. More evidence is necessary to determine the role of Ihh in articular cartilage and if a similar feedback cycle exists as previously described for the growth plate.
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Affiliation(s)
- Stacy A Semevolos
- Comparative Orthopaedics Laboratory, College of Veterinary Medicine, Cornell University, C3-187 Veterinary Medical Ctr, Ithaca, NY 14853, USA
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Abstract
The feasibility of articular gene therapy using insulin-like growth factor-I transgene expression in synovial tissues was assessed in vitro by transfection of synovial explant and monolayer cultures. Synovial membrane was harvested from horses and distributed for explant culture in multiwell plates or digested for monolayer culture in multiwell plates and chamber slides. Synovial monolayers were cultured for 48 h after infection with 0, 100, 200, or 500 moi adenovirus-IGF-I (AdeIGF-I) to establish an optimum dose. Explants were then either infected with AdeIGF-I or adenoviral LacZ and cultured for 8 days, treated with 100 ng/ml recombinant IGF-I as a positive control, or remained as uninfected untreated culture controls. Expression of IGF-I in explants and monolayers was assessed by in situ hybridization and quantitative polymerase chain reaction (PCR), and translation confirmed by IGF-I radioimmunoassay (RIA) and tissue immunoreaction. Effects of IGF-I on synovial function was assessed by proteoglycan and hyaluronan assay, and northern blot assessment of decorin and collagen type I expression. Significant transgene expression in synovial cells was present for all AdeIGF-I concentrations. Similarly, medium IGF-I concentrations were significantly elevated in AdeIGF-I infected synovial monolayer and explant cultures at all time points. Peak IGF-I concentration of 246 +/- 43 ng/ml developed in explant cultures on day 4; IGF-I levels in control explant groups were unchanged over baseline values. In situ hybridization and immunolocalization for IGF-I indicated focal IGF-I expression in intimal and subintimal layers of infected explants, with diffuse immunoreaction throughout infected subintimal and fibrous layers. For monolayer cultures, intracellular immunoreaction to IGF-I was markedly higher in infected cells, and was most prominent at 100 moi. Effects of IGF-I on synoviocyte cultures were evident on northern blots, which showed decreased decorin expression and elevated type I collagen production in AdeIGF-I infected monolayers. Proteoglycan concentration in the medium from explant cultures rose over the initial 4 days but was similar between treatment groups. The concentration of hyaluronan in medium from explant cultures did not differ significantly within or between treated and control groups during the 8-day study period. These data indicate that IGF-I can be successfully introduced to synovial structures by adenoviral vectors and results in effective IGF-I ligand synthesis without untoward synovial morphologic effects.
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Affiliation(s)
- R A Saxer
- Comparative Orthopaedics Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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Worster AA, Brower-Toland BD, Fortier LA, Bent SJ, Williams J, Nixon AJ. Chondrocytic differentiation of mesenchymal stem cells sequentially exposed to transforming growth factor-beta1 in monolayer and insulin-like growth factor-I in a three-dimensional matrix. J Orthop Res 2001; 19:738-49. [PMID: 11518286 DOI: 10.1016/s0736-0266(00)00054-1] [Citation(s) in RCA: 215] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This study evaluated chondrogenesis of mesenchymal progenitor stem cells (MSCs) cultured initially under pre-confluent monolayer conditions exposed to transforming growth factor-beta1 (TGF-beta1), and subsequently in three-dimensional cultures containing insulin-like growth factor I (IGF-I). Bone marrow aspirates and chondrocytes were obtained from horses and cultured in monolayer with 0 or 5 ng of TGF-beta 1 per ml of medium for 6 days. TGF-beta 1 treated and untreated cultures were distributed to three-dimensional fibrin disks containing 0 or 100 ng of IGF-I per ml of medium to establish four treatment groups. After 13 days, cultures were assessed by toluidine blue staining, collagen types I and II in situ hybridization and immunohistochemistry, proteoglycan production by [35S]-sulfate incorporation, and disk DNA content by fluorometry. Mesenchymal cells in monolayer cultures treated with TGF-beta1 actively proliferated for the first 4 days, developed cellular rounding, and formed cell clusters. Treated MSC cultures had a two-fold increase in medium proteoglycan content. Pretreatment of MSCs with TGF-beta1 followed by exposure of cells to IGF-I in three-dimensional culture significantly increased the formation of markers of chondrocytic function including disk proteoglycan content and procollagen type II mRNA production. However, proteoglycan and procollagen type II production by MSC's remained lower than parallel chondrocyte cultures. MSC pretreatment with TGF-beta1 without sequential IGF-I was less effective in initiating expression of markers of chondrogenesis. This study indicates that although MSC differentiation was less than complete when compared to mature chondrocytes, chondrogenesis was observed in IGF-I supplemented cultures, particularly when used in concert with TGF-beta1 pretreatment.
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Affiliation(s)
- A A Worster
- Comparative Orthopaedics Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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Abstract
Cartilage function after resurfacing with cell-based transplantation procedures or during the early stages of arthritic disease may be bolstered by the addition of growth factor genes to the transplanted tissue. Insulinlike growth factor-I maintains chondrocyte metabolism in normal cartilage homeostasis and has been shown to improve cartilage healing in vivo. Given the relatively short half-life of insulinlike growth factor-I in biologic systems, however, maintenance of effective concentrations of this peptide has necessitated either very high initial doses or repeated treatment. Delivery of the insulinlike growth factor-I gene, using a deleted adenovirus vector, specifically targeting graftable articular chondrocytes, bone marrow-derived chondroprogenitor cells, or synovial lining cells, may provide more durable insulinlike growth factor-I fluxes to articular tissues. Cultured equine articular chondrocytes, mesenchymal stem cells, synovial explants, and synovial intimal cells were readily transfected with an E1-deleted adenoviral vector containing equine insulinlike growth factor-I coding sequence. Optimal viral concentrations for effective transduction were 100 multiplicities of infection in synoviocytes, 500 multiplicities of infection in chondrocytes, and 1000 multiplicities of infection in mesenchymal stem cells. Production of insulinlike growth factor-I ligand varied from 65 ng/mL to 246 ng/mL in medium from chondrocytes and synovial explants, respectively. For chondrocytes, these concentrations were sufficient to produce significant stimulation of cartilage matrix gene expression and subsequent proteoglycan production. Moreover, cells in infected cultures maintained a chondrocytic phenotype and continued to express elevated insulinlike growth factor-I levels during 28 days of monolayer culture. Minimal synthetic activity, other than insulinlike growth factor-I ligand synthesis, was evident in synovial cultures. These experiments suggest several avenues for insulinlike growth factor-I supplementation of articular cartilage, including preimplantation adenoviral-insulinlike growth factor gene transfer to chondrocytes or chondroprogenitor cells, and direct injection of adenoviral-insulinlike growth factor to transfect the synovial structures in situ.
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Affiliation(s)
- A J Nixon
- Comparative Orthopaedics Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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