401
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Nguyen HDT, Sultana T, Kesanakurti P, Hambleton S. Genome sequencing and comparison of five Tilletia species to identify candidate genes for the detection of regulated species infecting wheat. IMA Fungus 2019; 10:11. [PMID: 32355611 PMCID: PMC7184893 DOI: 10.1186/s43008-019-0011-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/06/2019] [Indexed: 11/16/2022] Open
Abstract
Tilletia species cause diseases on grass hosts with some causing bunt diseases on wheat (Triticum). Two of the four species infecting wheat have restricted distributions globally and are subject to quarantine regulations to prevent their spread to new areas. Tilletia indica causes Karnal bunt and is regulated by many countries while the non-regulated T. walkeri is morphologically similar and very closely related phylogenetically, but infects ryegrass (Lolium) and not wheat. Tilletia controversa causes dwarf bunt of wheat (DB) and is also regulated by some countries, while the closely related but non-regulated species, T. caries and T. laevis, both cause common bunt of wheat (CB). Historically, diagnostic methods have relied on cryptic morphology to differentiate these species in subsamples from grain shipments. Of the DNA-based methods published so far, most have focused on sequence variation among tested strains at a single gene locus. To facilitate the development of additional molecular assays for diagnostics, we generated whole genome data for multiple strains of the two regulated wheat pathogens and their closest relatives. Depending on the species, the genomes were assembled into 907 to 4633 scaffolds ranging from 24 Mb to 30 Mb with 7842 to 9952 gene models predicted. Phylogenomic analyses confirmed the placement of Tilletia in the Exobasidiomycetes and showed that T. indica and T. walkeri were in one clade whereas T. controversa, T. caries and T. laevis grouped in a separate clade. Single copy and species-specific genes were identified by orthologous group analysis. Unique species-specific genes were identified and evaluated as suitable markers to differentiate the quarantine and non-quarantine species. After further analyses and manual inspection, primers and probes for the optimum candidate genes were designed and tested in silico, for validation in future wet-lab studies.
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Affiliation(s)
- Hai D. T. Nguyen
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6 Canada
| | - Tahera Sultana
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6 Canada
- Present Address: Research Farm – Vineland, London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Avenue N., Vineland Station, Ontario L0R 2E0 Canada
| | - Prasad Kesanakurti
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6 Canada
- Present Address: NHP Research Alliance, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 Canada
| | - Sarah Hambleton
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6 Canada
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402
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Dippenaar A, De Vos M, Marx FM, Adroub SA, van Helden PD, Pain A, Sampson SL, Warren RM. Whole genome sequencing provides additional insights into recurrent tuberculosis classified as endogenous reactivation by IS6110 DNA fingerprinting. INFECTION GENETICS AND EVOLUTION 2019; 75:103948. [PMID: 31276801 DOI: 10.1016/j.meegid.2019.103948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/22/2019] [Accepted: 06/30/2019] [Indexed: 12/21/2022]
Abstract
Recurrent tuberculosis (TB) after successful TB treatment occurs due to endogenous reactivation (relapse) or exogenous reinfection. We revisited the conclusions of relapse in a high TB incidence setting that were drawn on the basis of IS6110 restriction fragment length polymorphism (RFLP) analysis in a large retrospective cohort study in suburban Cape Town, South Africa. Using whole genome sequencing (WGS), we undertook pair-wise genome comparison of Mycobacterium tuberculosis strains cultured from diagnostic sputum samples collected at the index and recurrent TB episode for 25 recurrent TB cases who had been classified as relapse based on identical DNA fingerprint patterns in the earlier study. We found that paired strain genome sequences were identical or showed minimal variant differences in 22 of 25 recurrent TB cases, consistent with relapse. One showed 20 variant differences, suggestive of exogenous reinfection. Two of the 25 had mixed infections, each with the index episode strain detected as the dominant strain at recurrence in one of these patients, the minority strain harboured drug-resistance conferring mutations (rpoB, katG). In conclusion, our study highlights the additional value of WGS for investigating recurrent TB in settings with high infection pressure and closely related circulating strains, where the extent of re- and mixed infection may be underestimated.
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Affiliation(s)
- Anzaan Dippenaar
- NRF/DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - Margaretha De Vos
- NRF/DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Florian M Marx
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; DST-NRF South African Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Sabir A Adroub
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Paul D van Helden
- NRF/DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Samantha L Sampson
- NRF/DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M Warren
- NRF/DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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403
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O'Neill MB, Shockey A, Zarley A, Aylward W, Eldholm V, Kitchen A, Pepperell CS. Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia. Mol Ecol 2019; 28:3241-3256. [PMID: 31066139 PMCID: PMC6660993 DOI: 10.1111/mec.15120] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/29/2022]
Abstract
Mycobacterium tuberculosis (M.tb) is a globally distributed, obligate pathogen of humans that can be divided into seven clearly defined lineages. An emerging consensus places the origin and global dispersal of M.tb within the past 6,000 years: identifying how the ancestral clone of M.tb spread and differentiated within this timeframe is important for identifying the ecological drivers of the current pandemic. We used Bayesian phylogeographic inference to reconstruct the migratory history of M.tb in Africa and Eurasia and to investigate lineage specific patterns of spread from a geographically diverse sample of 552 M.tb genomes. Applying evolutionary rates inferred with ancient M.tb genome calibration, we estimated the timing of major events in the migratory history of the pathogen. Inferred timings contextualize M.tb dispersal within historical phenomena that altered patterns of connectivity throughout Africa and Eurasia: trans-Indian Ocean trade in spices and other goods, the Silk Road and its predecessors, the expansion of the Roman Empire, and the European Age of Exploration. We found that Eastern Africa and Southeast Asia have been critical in the dispersal of M.tb. Our results further reveal that M.tb populations have grown through range expansion, as well as in situ, and delineate the independent evolutionary trajectories of bacterial subpopulations underlying the current pandemic.
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Affiliation(s)
- Mary B. O'Neill
- Laboratory of GeneticsUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of Medical Microbiology and ImmunologyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Present address:
Unit of Human Evolutionary GeneticsInstitut PasteurParisFrance
| | - Abigail Shockey
- Department of Medical Microbiology and ImmunologyUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Alex Zarley
- Department of GeographyUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - William Aylward
- Department of Classical and Ancient Near Eastern StudiesUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Vegard Eldholm
- Infection Control and Environmental HealthNorwegian Institute of Public HealthOsloNorway
| | - Andrew Kitchen
- Department of AnthropologyUniversity of IowaIowa CityIAUSA
| | - Caitlin S. Pepperell
- Department of Medical Microbiology and ImmunologyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of MedicineUniversity of Wisconsin‐MadisonMadisonWIUSA
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404
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Gyuris A, Navarrete-Perea J, Jo A, Cristea S, Zhou S, Fraser K, Wei Z, Krichevsky AM, Weissleder R, Lee H, Gygi SP, Charest A. Physical and Molecular Landscapes of Mouse Glioma Extracellular Vesicles Define Heterogeneity. Cell Rep 2019; 27:3972-3987.e6. [PMID: 31242427 PMCID: PMC6604862 DOI: 10.1016/j.celrep.2019.05.089] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/15/2019] [Accepted: 05/22/2019] [Indexed: 12/21/2022] Open
Abstract
Cancer extracellular vesicles (EVs) are highly heterogeneous, which impedes our understanding of their function as intercellular communication agents and biomarkers. To deconstruct this heterogeneity, we analyzed extracellular RNAs (exRNAs) and extracellular proteins (exPTNs) from size fractionation of large, medium, and small EVs and ribonucleoprotein complexes (RNPs) from mouse glioblastoma cells by RNA sequencing and quantitative proteomics. mRNA from medium-sized EVs most closely reflects the cellular transcriptome, whereas small EV exRNA is enriched in small non-coding RNAs and RNPs contain precisely processed tRNA fragments. The exPTN composition of EVs and RNPs reveals that they are closely related by vesicle type, independent of their cellular origin, and single EV analysis reveals that small EVs are less heterogeneous in their protein content than larger ones. We provide a foundation for better understanding of segregation of macromolecules in glioma EVs through a catalog of diverse exRNAs and exPTNs.
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Affiliation(s)
- Aron Gyuris
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | | | - Ala Jo
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Simona Cristea
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Shuang Zhou
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kyle Fraser
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Zhiyun Wei
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Initiative for RNA Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Anna M Krichevsky
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Initiative for RNA Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Steve P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Al Charest
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.
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405
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Merkhofer RM, O'Neill MB, Xiong D, Hernandez-Santos N, Dobson H, Fites JS, Shockey AC, Wuethrich M, Pepperell CS, Klein BS. Investigation of Genetic Susceptibility to Blastomycosis Reveals Interleukin-6 as a Potential Susceptibility Locus. mBio 2019; 10:e01224-19. [PMID: 31213563 PMCID: PMC6581865 DOI: 10.1128/mbio.01224-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 12/12/2022] Open
Abstract
Genetic differences are hypothesized to underlie ethnic disparities in incidence rates of the endemic systemic mycoses, including blastomycosis. Individuals of Hmong ancestry display elevated risk for this serious fungal infection. Here, we interrogated the genomes of Wisconsin (WI) Hmong blastomycosis patients using homozygosity mapping to uncover regions of the genome that are likely shared among the greater Hmong population and filtered for variants with high potential to affect disease susceptibility. This approach uncovered 113 candidate susceptibility variants, and among the most promising are those in genes involved in the interleukin-17 (IL-17) response. In particular, we identified 25 linked variants near the gene encoding IL-6 (IL6). We validated differences in cytokine production between Hmong and European volunteers and formally demonstrated a critical role for IL-6 in the development of adaptive immunity to Blastomyces dermatitidis Our findings suggest that the dysregulation of IL-17 responses underlies a recently reported and poorly understood ethnic health disparity.IMPORTANCE Blastomycosis is a potentially life-threatening infection caused by the fungus Blastomyces dermatitidis As with related fungal diseases, blastomycosis is noted to affect some populations more than others. These patterns of illness are often not related to predisposing conditions or exposure risks; thus, genetic differences are thought to underlie these health disparities. People of Hmong ancestry in Wisconsin are at elevated risk of blastomycosis compared to the general population. We studied the genetic codes of Hmong blastomycosis patients and identified candidate sites in their genomes that may explain their susceptibility to this infection. We further studied one particular region of the genome that is involved with the immune processes that fight B. dermatitidis Our work revealed population differences in the response to fungi. A better understanding of the genetic underpinnings of susceptibility to infectious diseases has broader implications for community health, especially in the paradigm of personalized medicine.
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Affiliation(s)
- Richard M Merkhofer
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mary B O'Neill
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Donny Xiong
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nydiaris Hernandez-Santos
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Hannah Dobson
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - J Scott Fites
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Abigail C Shockey
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marcel Wuethrich
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Bruce S Klein
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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406
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Pavkovic M, Pantano L, Gerlach CV, Brutus S, Boswell SA, Everley RA, Shah JV, Sui SH, Vaidya VS. Multi omics analysis of fibrotic kidneys in two mouse models. Sci Data 2019; 6:92. [PMID: 31201317 PMCID: PMC6570759 DOI: 10.1038/s41597-019-0095-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
Kidney fibrosis represents an urgent unmet clinical need due to the lack of effective therapies and an inadequate understanding of the molecular pathogenesis. We have generated a comprehensive and combined multi-omics dataset (proteomics, mRNA and small RNA transcriptomics) of fibrotic kidneys that is searchable through a user-friendly web application: http://hbcreports.med.harvard.edu/fmm/. Two commonly used mouse models were utilized: a reversible chemical-induced injury model (folic acid (FA) induced nephropathy) and an irreversible surgically-induced fibrosis model (unilateral ureteral obstruction (UUO)). mRNA and small RNA sequencing, as well as 10-plex tandem mass tag (TMT) proteomics were performed with kidney samples from different time points over the course of fibrosis development. The bioinformatics workflow used to process, technically validate, and combine the single omics data will be described. In summary, we present temporal multi-omics data from fibrotic mouse kidneys that are accessible through an interrogation tool (Mouse Kidney Fibromics browser) to provide a searchable transcriptome and proteome for kidney fibrosis researchers. Design Type(s) | transcription profiling design • proteomic profiling design • stimulus or stress design | Measurement Type(s) | transcription profiling assay • protein expression profiling assay | Technology Type(s) | RNA sequencing • mass spectrometry | Factor Type(s) | experimental condition • temporal_instant • biological replicate | Sample Characteristic(s) | Mus musculus • kidney |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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Affiliation(s)
- Mira Pavkovic
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Medicine - Renal Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Lorena Pantano
- Bioinformatics Core, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Cory V Gerlach
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Medicine - Renal Division, Brigham and Women's Hospital, Boston, MA, USA.,Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sergine Brutus
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sarah A Boswell
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Robert A Everley
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jagesh V Shah
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Medicine - Renal Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Shannan H Sui
- Bioinformatics Core, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Vishal S Vaidya
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA. .,Department of Medicine - Renal Division, Brigham and Women's Hospital, Boston, MA, USA. .,Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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407
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Hemsley CM, O’Neill PA, Essex-Lopresti A, Norville IH, Atkins TP, Titball RW. Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups. BMC Genomics 2019; 20:441. [PMID: 31164106 PMCID: PMC6549354 DOI: 10.1186/s12864-019-5833-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coxiella burnetii is a zoonotic pathogen that resides in wild and domesticated animals across the globe and causes a febrile illness, Q fever, in humans. An improved understanding of the genetic diversity of C. burnetii is essential for the development of diagnostics, vaccines and therapeutics, but genotyping data is lacking from many parts of the world. Sporadic outbreaks of Q fever have occurred in the United Kingdom, but the local genetic make-up of C. burnetii has not been studied in detail. RESULTS Here, we report whole genome data for nine C. burnetii sequences obtained in the UK. All four genomes of C. burnetii from cattle, as well as one sheep sample, belonged to Multi-spacer sequence type (MST) 20, whereas the goat samples were MST33 (three genomes) and MST32 (one genome), two genotypes that have not been described to be present in the UK to date. We established the phylogenetic relationship between the UK genomes and 67 publically available genomes based on single nucleotide polymorphisms (SNPs) in the core genome, which confirmed tight clustering of strains within genomic groups, but also indicated that sub-groups exist within those groups. Variation is mainly achieved through SNPs, many of which are non-synonymous, thereby confirming that evolution of C. burnetii is based on modification of existing genes. Finally, we discovered genomic-group specific genome content, which supports a model of clonal expansion of previously established genotypes, with large scale dissemination of some of these genotypes across continents being observed. CONCLUSIONS The genetic make-up of C. burnetii in the UK is similar to the one in neighboring European countries. As a species, C. burnetii has been considered a clonal pathogen with low genetic diversity at the nucleotide level. Here, we present evidence for significant variation at the protein level between isolates of different genomic groups, which mainly affects secreted and membrane-associated proteins. Our results thereby increase our understanding of the global genetic diversity of C. burnetii and provide new insights into the evolution of this emerging zoonotic pathogen.
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Affiliation(s)
- Claudia M. Hemsley
- College of Life and Environmental Sciences – Biosciences, University of Exeter, Exeter, UK
| | - Paul A. O’Neill
- College of Life and Environmental Sciences – Biosciences, University of Exeter, Exeter, UK
| | | | | | - Tim P. Atkins
- College of Life and Environmental Sciences – Biosciences, University of Exeter, Exeter, UK
- Defence Science and Technology Laboratory, Porton Down, Salisbury, UK
| | - Richard W. Titball
- College of Life and Environmental Sciences – Biosciences, University of Exeter, Exeter, UK
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408
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A Computational Protocol to Analyze Metatranscriptomic Data Capturing Fungal-Host Interactions. Methods Mol Biol 2019; 1848:207-233. [PMID: 30182238 DOI: 10.1007/978-1-4939-8724-5_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Plant diseases cause significant losses to agricultural production and pose serious threats to food security worldwide. Understanding the mechanism of host-pathogen interaction is essential for the development of novel diagnostic methods and disease management strategies. RNA sequencing (or RNA-Seq) technology enables a global characterization and quantification of all transcripts of organisms from which RNA can be obtained, and it is particularly useful in identifying pathogen virulence factors involved in disease development and host immunity involved in the development of resistance. This chapter describes a computational protocol to manage, analyze and interpret RNA-Seq data. We have included two transcriptome analysis approaches, one reference-guided and the other de novo assembly-based, and discuss pros and cons for each method. We have also presented visualization methods to generate high quality figures as well as data mining strategies for identifying candidate genes/pathways involved in host immunity and pathogen virulence. In summary, this protocol captures the fungal-plant interactions at the transcriptional level and facilitates rapid gene discovery and expression analysis using next-generation sequencing data of mixed host and pathogen transcripts (i.e., metatranscriptomics). All bioinformatic tools used to build this protocol are publically available, and we strove to make them accessible to researchers with limited computational skills and applicable to metatranscriptomic data analysis in a wide range of plant-fungal interactions.
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409
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Strieskova L, Gazdaricova I, Kajsik M, Soltys K, Budis J, Pos O, Lickova M, Klempa B, Szemes T. Ultracentrifugation enrichment protocol followed by total RNA sequencing allows assembly of the complete mitochondrial genome. J Biotechnol 2019; 299:8-12. [PMID: 31022426 DOI: 10.1016/j.jbiotec.2019.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/18/2019] [Accepted: 04/20/2019] [Indexed: 12/23/2022]
Abstract
The mitochondrial genome is an independent genetic system in each eukaryotic cell outside the nuclear genome. Mitochondrial DNA (mtDNA) appears in high copy number within one cell, unlike nuclear DNA, which exists in two copies. But nevertheless, mtDNA represent only small part of total cellular DNA what causes problematic analysis and identification of relevant mutations. While most researchers tend to overlook it because of its small size, the mitochondrial genome contains genes that are essential for cellular energetics and survival. Because of the increased awareness on the importance of metabolism and bioenergetics in a wide variety of human diseases, more and more mtDNA studies were performed. Mitochondrial genome research has established the connection between mtDNA and a wide variety of diseases such as cancer or neurodegenerative disorders. At the present time, several methods are known, that allow sequencing of mtDNA. However, genomic analysis is often complicated due to the low content of mtDNA compared to nuclear DNA. For this reason, we have designed a new approach to obtaining the genomic mitochondrial sequence. We chose RNA based sequencing. Since human mtDNA does not contain introns, the reconstruction of whole mitochondrial genome through RNA sequencing seems to be effective. Our method is based on total RNA sequencing coupled with simple ultracentrifugation protocol and de novo assembly. Following our protocol, we were able to assemble a complete mammalian mitochondrial genome with a length of 16,505 bp and an average coverage of 156. The method is a relatively simple and inexpensive which could help in the further research or diagnostics of mtDNA-based diseases.
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Affiliation(s)
| | - Iveta Gazdaricova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Michal Kajsik
- Comenius University Science Park, Bratislava, Slovakia
| | - Katarina Soltys
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia
| | - Jaroslav Budis
- Geneton Ltd., Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia; Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | - Ondrej Pos
- Geneton Ltd., Bratislava, Slovakia; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.
| | - Martina Lickova
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Tomas Szemes
- Geneton Ltd., Bratislava, Slovakia; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia
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410
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McMillan EA, Gupta SK, Williams LE, Jové T, Hiott LM, Woodley TA, Barrett JB, Jackson CR, Wasilenko JL, Simmons M, Tillman GE, McClelland M, Frye JG. Antimicrobial Resistance Genes, Cassettes, and Plasmids Present in Salmonella enterica Associated With United States Food Animals. Front Microbiol 2019; 10:832. [PMID: 31057528 PMCID: PMC6479191 DOI: 10.3389/fmicb.2019.00832] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/01/2019] [Indexed: 11/13/2022] Open
Abstract
The ability of antimicrobial resistance (AR) to transfer, on mobile genetic elements (MGEs) between bacteria, can cause the rapid establishment of multidrug resistance (MDR) in bacteria from animals, thus creating a foodborne risk to human health. To investigate MDR and its association with plasmids in Salmonella enterica, whole genome sequence (WGS) analysis was performed on 193 S. enterica isolated from sources associated with United States food animals between 1998 and 2011; 119 were resistant to at least one antibiotic tested. Isolates represented 86 serotypes and variants, as well as diverse phenotypic resistance profiles. A total of 923 AR genes and 212 plasmids were identified among the 193 strains. Every isolate contained at least one AR gene. At least one plasmid was detected in 157 isolates. Genes were identified for resistance to aminoglycosides (n = 472), β-lactams (n = 84), tetracyclines (n = 171), sulfonamides (n = 91), phenicols (n = 42), trimethoprim (n = 8), macrolides (n = 5), fosfomycin (n = 48), and rifampicin (n = 2). Plasmid replicon types detected in the isolates were A/C (n = 32), ColE (n = 76), F (n = 43), HI1 (n = 4), HI2 (n = 20), I1 (n = 62), N (n = 4), Q (n = 7), and X (n = 35). Phenotypic resistance correlated with the AR genes identified in 95.4% of cases. Most AR genes were located on plasmids, with many plasmids harboring multiple AR genes. Six antibiotic resistance cassette structures (ARCs) and one pseudo-cassette were identified. ARCs contained between one and five resistance genes (ARC1: sul2, strAB, tetAR; ARC2: aac3-iid; ARC3: aph, sph; ARC4: cmy-2; ARC5: floR; ARC6: tetB; pseudo-ARC: aadA, aac3-VIa, sul1). These ARCs were present in multiple isolates and on plasmids of multiple replicon types. To determine the current distribution and frequency of these ARCs, the public NCBI database was analyzed, including WGS data on isolates collected by the USDA Food Safety and Inspection Service (FSIS) from 2014 to 2018. ARC1, ARC4, and ARC5 were significantly associated with cattle isolates, while ARC6 was significantly associated with chicken isolates. This study revealed that a diverse group of plasmids, carrying AR genes, are responsible for the phenotypic resistance seen in Salmonella isolated from United States food animals. It was also determined that many plasmids carry similar ARCs.
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Affiliation(s)
| | - Sushim K Gupta
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - Laura E Williams
- Department of Biology, Providence College, Providence, RI, United States
| | - Thomas Jové
- INSERM, CHU Limoges, RESINFIT, University of Limoges, Limoges, France
| | - Lari M Hiott
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - Tiffanie A Woodley
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - John B Barrett
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - Charlene R Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - Jamie L Wasilenko
- Eastern Lab, United States Department of Agriculture, Food Safety and Inspection Service, Athens, GA, United States
| | - Mustafa Simmons
- Eastern Lab, United States Department of Agriculture, Food Safety and Inspection Service, Athens, GA, United States
| | - Glenn E Tillman
- Eastern Lab, United States Department of Agriculture, Food Safety and Inspection Service, Athens, GA, United States
| | - Michael McClelland
- Department of Microbiology & Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
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411
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Iyer P, Shrikhande SV, Ranjan M, Joshi A, Gardi N, Prasad R, Dharavath B, Thorat R, Salunkhe S, Sahoo B, Chandrani P, Kore H, Mohanty B, Chaudhari V, Choughule A, Kawle D, Chaudhari P, Ingle A, Banavali S, Gera P, Ramadwar MR, Prabhash K, Barreto SG, Dutt S, Dutt A. ERBB2 and KRAS alterations mediate response to EGFR inhibitors in early stage gallbladder cancer. Int J Cancer 2019; 144:2008-2019. [PMID: 30304546 PMCID: PMC6378102 DOI: 10.1002/ijc.31916] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 09/27/2018] [Indexed: 02/05/2023]
Abstract
The uncommonness of gallbladder cancer in the developed world has contributed to the generally poor understanding of the disease. Our integrated analysis of whole exome sequencing, copy number alterations, immunohistochemical, and phospho-proteome array profiling indicates ERBB2 alterations in 40% early-stage rare gallbladder tumors, among an ethnically distinct population not studied before, that occurs through overexpression in 24% (n = 25) and recurrent mutations in 14% tumors (n = 44); along with co-occurring KRAS mutation in 7% tumors (n = 44). We demonstrate that ERBB2 heterodimerizes with EGFR to constitutively activate the ErbB signaling pathway in gallbladder cells. Consistent with this, treatment with ERBB2-specific, EGFR-specific shRNA or with a covalent EGFR family inhibitor Afatinib inhibits tumor-associated characteristics of the gallbladder cancer cells. Furthermore, we observe an in vivo reduction in tumor size of gallbladder xenografts in response to Afatinib is paralleled by a reduction in the amounts of phospho-ERK, in tumors harboring KRAS (G13D) mutation but not in KRAS (G12V) mutation, supporting an essential role of the ErbB pathway. In overall, besides implicating ERBB2 as an important therapeutic target under neo-adjuvant or adjuvant settings, we present the first evidence that the presence of KRAS mutations may preclude gallbladder cancer patients to respond to anti-EGFR treatment, similar to a clinical algorithm commonly practiced to opt for anti-EGFR treatment in colorectal cancer.
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Affiliation(s)
- Prajish Iyer
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
| | - Shailesh V. Shrikhande
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
- Department of Gastrointestinal and Hepato‐Pancreato‐Biliary Surgical OncologyTata Memorial Centre, Ernest Borges MargMumbaiMaharashtraIndia
| | - Malika Ranjan
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Asim Joshi
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
| | - Nilesh Gardi
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Ratnam Prasad
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Bhasker Dharavath
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
| | - Rahul Thorat
- Laboratory Animal FacilityAdvanced Centre for Treatment, Research and Education in Cancer, Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Sameer Salunkhe
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
- Shilpee laboratoryAdvanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Bikram Sahoo
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Pratik Chandrani
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Hitesh Kore
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Bhabani Mohanty
- Small Animal Imaging facilityAdvanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Vikram Chaudhari
- Department of Gastrointestinal and Hepato‐Pancreato‐Biliary Surgical OncologyTata Memorial Centre, Ernest Borges MargMumbaiMaharashtraIndia
| | - Anuradha Choughule
- Department of Medical OncologyTata Memorial Centre, Ernest Borges MargMumbaiMaharashtraIndia
| | - Dhananjay Kawle
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Pradip Chaudhari
- Small Animal Imaging facilityAdvanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Arvind Ingle
- Laboratory Animal FacilityAdvanced Centre for Treatment, Research and Education in Cancer, Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Shripad Banavali
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
- Department of Medical OncologyTata Memorial Centre, Ernest Borges MargMumbaiMaharashtraIndia
| | - Poonam Gera
- Tissue BiorepositoryAdvanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Mukta R. Ramadwar
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
- Department of PathologyTata Memorial Centre, Ernest Borges MargMumbaiMaharashtraIndia
| | - Kumar Prabhash
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
- Department of Medical OncologyTata Memorial Centre, Ernest Borges MargMumbaiMaharashtraIndia
| | - Savio George Barreto
- Department of Gastrointestinal and Hepato‐Pancreato‐Biliary Surgical OncologyTata Memorial Centre, Ernest Borges MargMumbaiMaharashtraIndia
| | - Shilpee Dutt
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
- Shilpee laboratoryAdvanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Amit Dutt
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
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412
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Tan CCS, Maurer-Stroh S, Wan Y, Sessions OM, de Sessions PF. A novel method for the capture-based purification of whole viral native RNA genomes. AMB Express 2019; 9:45. [PMID: 30963294 PMCID: PMC6453989 DOI: 10.1186/s13568-019-0772-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 04/02/2019] [Indexed: 01/06/2023] Open
Abstract
Current technologies for targeted characterization and manipulation of viral RNA primarily involve amplification or ultracentrifugation with isopycnic gradients of viral particles to decrease host RNA background. The former strategy is non-compatible for characterizing properties innate to RNA strands such as secondary structure, RNA-RNA interactions, and also for nanopore direct RNA sequencing involving the sequencing of native RNA strands. The latter strategy, ultracentrifugation, causes loss in genomic information due to its inability to retrieve unassembled viral RNA. To address this, we developed a novel application of current nucleic acid hybridization technologies for direct characterization of RNA. In particular, we modified a current enrichment protocol to capture whole viral native RNA genomes for downstream RNA assays to circumvent the abovementioned problems. This technique involves hybridization of biotinylated baits at 500 nucleotides (nt) intervals, stringent washes and release of free native RNA strands using DNase I treatment, with a turnaround time of about 6 h 15 min. RT-qPCR was used as the primary proof of concept that capture-based purification indeed removes host background. Subsequently, capture-based purification was applied to direct RNA sequencing as proof of concept that capture-based purification can be coupled with downstream RNA assays. We report that this protocol was able to successfully purify viral RNA by 561- to 791-fold. We also report that application of this protocol to direct RNA sequencing yielded a reduction in human host RNA background by 1580-fold, a 99.91% recovery of viral genome with at least 15× coverage, and a mean coverage across the genome of 120×. This report is, to the best of our knowledge, the first description of a capture-based purification method for assays that involve direct manipulation or characterisation of native RNA. This report also describes a successful application of capture-based purification as a direct RNA sequencing strategy that addresses certain limitations of current strategies in sequencing RNA viral genomes.
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Affiliation(s)
- Cedric Chih Shen Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- A*STAR Graduate Academy, Singapore, Singapore
- University College London, London, UK
| | | | - Yue Wan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Paola Florez de Sessions
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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413
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Integrative immunologic and genomic characterization of brain metastasis from ovarian/peritoneal cancer. Pathol Res Pract 2019; 215:152404. [PMID: 30962002 DOI: 10.1016/j.prp.2019.03.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/13/2019] [Accepted: 03/31/2019] [Indexed: 12/13/2022]
Abstract
Brain metastasis from ovarian/peritoneal cancer is a rare disease that has a dismal prognosis. And genomic alterations and immune-profiling in primary ovarian/ peritoneal cancer and brain metastatic tumor tissues have not been fully elucidated. Multiplexed immunofluorescence and whole-exome sequencing of two matched brain metastatic tumor and primary ovarian/peritoneal cancer tissues were performed. The overall density of immune infiltrates in metastatic tissues (brain) was not significantly different from those in primary cancer tissues (case 1 primary: 2.12% and case 1 metastasis: 2.22%; case 2 primary: 1.70%, and case 2 metastasis: 3.46%). Of note, however, PD-L1 expression in the metastases was higher than that in the primary tumors. We found more non-silent mutations, cancer-related genes, loss of heterozygosity (LOH) and longer lengths of copy-number alterations (CNA) in brain metastases compared to primary ovarian/peritoneal cancers. We report immunologic and genomic profiles of primary ovarian/peritoneal cancer with brain metastasis that may not only provide useful information for understanding its pathogenesis, but also clues for further innovative therapeutic treatments for ovarian cancer.
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414
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Lin S, Yu L, Zhang H. Transcriptomic Responses to Thermal Stress and Varied Phosphorus Conditions in Fugacium kawagutii. Microorganisms 2019; 7:microorganisms7040096. [PMID: 30987028 PMCID: PMC6517890 DOI: 10.3390/microorganisms7040096] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/18/2019] [Accepted: 03/30/2019] [Indexed: 01/08/2023] Open
Abstract
Coral reef-associated Symbiodiniaceae live in tropical and oligotrophic environments and are prone to heat and nutrient stress. How their metabolic pathways respond to pulses of warming and phosphorus (P) depletion is underexplored. Here, we conducted RNA-seq analysis to investigate transcriptomic responses to thermal stress, phosphate deprivation, and organic phosphorus (OP) replacement in Fugacium kawagutii. Using dual-algorithm (edgeR and NOIseq) to remedy the problem of no replicates, we conservatively found 357 differentially expressed genes (DEGs) under heat stress, potentially regulating cell wall modulation and the transport of iron, oxygen, and major nutrients. About 396 DEGs were detected under P deprivation and 671 under OP utilization, both mostly up-regulated and potentially involved in photosystem and defensome, despite different KEGG pathway enrichments. Additionally, we identified 221 genes that showed relatively stable expression levels across all conditions (likely core genes), mostly catalytic and binding proteins. This study reveals a wide range of, and in many cases previously unrecognized, molecular mechanisms in F. kawagutii to cope with heat stress and phosphorus-deficiency stress. Their quantitative expression dynamics, however, requires further verification with triplicated experiments, and the data reported here only provide clues for generating testable hypotheses about molecular mechanisms underpinning responses and adaptation in F. kawagutii to temperature and nutrient stresses.
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Affiliation(s)
- Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, China.
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
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415
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John J, Kukshal P, Sharma A, Bhatia T, Nimgaonkar VL, Deshpande SN, Thelma BK. Rare variants in Protein tyrosine phosphatase, receptor type A (PTPRA) in schizophrenia: Evidence from a family based study. Schizophr Res 2019; 206:75-81. [PMID: 30594456 PMCID: PMC7321970 DOI: 10.1016/j.schres.2018.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/25/2018] [Accepted: 12/08/2018] [Indexed: 12/23/2022]
Abstract
The contribution of both common and rare risk variants to the genetic architecture of schizophrenia (SZ) has been documented in genome-wide association studies, whole exome and whole genome sequencing approaches. As SZ is highly heritable and segregates in families, highly penetrant rare variants are more likely to be identified through analyses of multiply affected families. Further, much of the gene mapping studies in SZ have utilized individuals of Caucasian ancestry. Analysis of other ethnic groups may be informative. In this study, we aimed at identification of rare, penetrant risk variants utilizing whole exome sequencing (WES) in a three-generation Indian family with multiple members affected. Filtered data from WES, combined with in silico analyses revealed a novel heterozygous missense variant (NM_080841:c.1730C>G:p.T577R; exon18) in Protein tyrosine phosphatase, receptor type A (PTPRA 20p13). The variant was located in an evolutionarily conserved position and predicted to be damaging. Screening for variants in this gene in the WES data of an independent SZ cohort (n = 350) of matched ethnicity, identified five additional rare missense variants with MAF < 0.003, which were also predicted to be damaging. In conclusion, the rare missense variants in PTPRA identified in this study could confer risk for SZ. This has also derived support from concordant data from prior linkage and association, as well as animal studies which indicated a role for PTPRA in glutamate function.
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Affiliation(s)
- Jibin John
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Prachi Kukshal
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Aditya Sharma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Triptish Bhatia
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - V L Nimgaonkar
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, 3811 O'Hara Street, Pittsburgh, PA 15213, USA; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, DeSoto St, Pittsburgh, PA 15213, USA
| | - S N Deshpande
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India.
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416
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Mitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen Phytophthora ramorum. mBio 2019; 10:mBio.02452-18. [PMID: 30862749 PMCID: PMC6414701 DOI: 10.1128/mbio.02452-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Alien species are often successful invaders in new environments, despite the introduction of a few isolates with a reduced genetic pool. This is called the genetic paradox of invasion. We found two mechanisms by which the invasive forest pathogen causing sudden oak and sudden larch death can evolve. Extensive mitotic recombination producing runs of homozygosity generates genotypic diversity even in the absence of sexual reproduction, and rapid turnover of genes in the non-core, or nonessential portion of genome not shared by all isolates, allows pathogenicity genes to evolve rapidly or be eliminated while retaining essential genes. Mitotic recombination events occur in genomic hot spots, resulting in similar ROH patterns in different isolates or groups; one ROH, independently generated in two different groups, was enriched in pathogenicity genes and may be a target for selection. This provides important insights into the evolution of invasive alien pathogens and their potential for adaptation and future persistence. Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic paradox of invasion. Phytophthora ramorum is invasive, limited to asexual reproduction within four lineages, and presumed clonal. It is responsible for sudden oak death in the United States, sudden larch death in Europe, and ramorum blight in North America and Europe. We sequenced the genomes of 107 isolates to determine how this pathogen can overcome the invasion paradox. Mitotic recombination (MR) associated with transposons and low gene density has generated runs of homozygosity (ROH) affecting 2,698 genes, resulting in novel genotypic diversity within the lineages. One ROH enriched in effectors was fixed in the NA1 lineage. An independent ROH affected the same scaffold in the EU1 lineage, suggesting an MR hot spot and a selection target. Differences in host infection between EU1 isolates with and without the ROH suggest that they may differ in aggressiveness. Non-core regions (not shared by all lineages) had signatures of accelerated evolution and were enriched in putative pathogenicity genes and transposons. There was a striking pattern of gene loss, including all effectors, in the non-core EU2 genome. Positive selection was observed in 8.0% of RxLR and 18.8% of Crinkler effector genes compared with 0.9% of the core eukaryotic gene set. We conclude that the P. ramorum lineages are diverging via a rapidly evolving non-core genome and that the invasive asexual lineages are not clonal, but display genotypic diversity caused by MR.
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417
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Colgan TJ, Fletcher IK, Arce AN, Gill RJ, Ramos Rodrigues A, Stolle E, Chittka L, Wurm Y. Caste- and pesticide-specific effects of neonicotinoid pesticide exposure on gene expression in bumblebees. Mol Ecol 2019; 28:1964-1974. [PMID: 30843300 PMCID: PMC6563198 DOI: 10.1111/mec.15047] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 01/10/2023]
Abstract
Social bees are important insect pollinators of wildflowers and agricultural crops, making their reported declines a global concern. A major factor implicated in these declines is the widespread use of neonicotinoid pesticides. Indeed, recent research has demonstrated that exposure to low doses of these neurotoxic pesticides impairs bee behaviours important for colony function and survival. However, our understanding of the molecular-genetic pathways that lead to such effects is limited, as is our knowledge of how effects may differ between colony members. To understand what genes and pathways are affected by exposure of bumblebee workers and queens to neonicotinoid pesticides, we implemented a transcriptome-wide gene expression study. We chronically exposed Bombus terrestriscolonies to either clothianidin or imidacloprid at field-realistic concentrations while controlling for factors including colony social environment and worker age. We reveal that genes involved in important biological processes including mitochondrial function are differentially expressed in response to neonicotinoid exposure. Additionally, clothianidin exposure had stronger effects on gene expression amplitude and alternative splicing than imidacloprid. Finally, exposure affected workers more strongly than queens. Our work demonstrates how RNA-Seq transcriptome profiling can provide detailed novel insight on the mechanisms mediating pesticide toxicity to a key insect pollinator.
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Affiliation(s)
- Thomas J Colgan
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.,School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Isabel K Fletcher
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Andres N Arce
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Richard J Gill
- Department of Life Sciences, Imperial College London, Ascot, UK
| | | | - Eckart Stolle
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Lars Chittka
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Yannick Wurm
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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418
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Huang W, Chen X, Guan Q, Zhong Z, Ma J, Yang B, Wang T, Zhu W, Tian J. Changes of alternative splicing in Arabidopsis thaliana grown under different CO2 concentrations. Gene 2019; 689:43-50. [DOI: 10.1016/j.gene.2018.11.083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 11/09/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
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419
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Abstract
As a major biomarker of liquid biopsy, cell-free tumor DNA (ctDNA), which can be extracted from blood, urine, or other circulating liquids, is able to provide comprehensive genetic information of tumor and better overcome the tumor heterogeneity problem comparing to tissue biopsy. Developed in recent years, next-generation sequencing (NGS) is a widely used technology for analyzing ctDNA. Although the technologies of processing ctDNA samples are mature, the task to detect low mutated allele frequency (MAF) variations from noisy sequencing data remains challenging. In this chapter, the authors will first explain the difficulties of analyzing ctDNA sequencing data, review related technologies, and then present some novel bioinformatics methods for analyzing ctDNA NGS data in better ways.
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420
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Yücel O, Borgert SR, Poehlein A, Niermann K, Philipp B. The 7α-hydroxysteroid dehydratase Hsh2 is essential for anaerobic degradation of the steroid skeleton of 7α-hydroxyl bile salts in the novel denitrifying bacterium Azoarcus sp. strain Aa7. Environ Microbiol 2019; 21:800-813. [PMID: 30680854 DOI: 10.1111/1462-2920.14508] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 12/24/2022]
Abstract
Bile salts are steroid compounds from the digestive tract of vertebrates and enter the environment via defecation. Many aerobic bile-salt degrading bacteria are known but no bacteria that completely degrade bile salts under anoxic conditions have been isolated so far. In this study, the facultatively anaerobic Betaproteobacterium Azoarcus sp. strain Aa7 was isolated that grew with bile salts as sole carbon source under anoxic conditions with nitrate as electron acceptor. Phenotypic and genomic characterization revealed that strain Aa7 used the 2,3-seco pathway for the degradation of bile salts as found in other denitrifying steroid-degrading bacteria such as Sterolibacterium denitrificans. Under oxic conditions strain Aa7 used the 9,10-seco pathway as found in, for example, Pseudomonas stutzeri Chol1. Metabolite analysis during anaerobic growth indicated a reductive dehydroxylation of 7α-hydroxyl bile salts. Deletion of the gene hsh2 Aa7 encoding a 7-hydroxysteroid dehydratase led to strongly impaired growth with cholate and chenodeoxycholate but not with deoxycholate lacking a hydroxyl group at C7. The hsh2 Aa7 deletion mutant degraded cholate and chenodeoxycholate to the corresponding C19 -androstadienediones only while no phenotype change was observed during aerobic degradation of cholate. These results showed that removal of the 7α-hydroxyl group was essential for cleavage of the steroid skeleton under anoxic conditions.
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Affiliation(s)
- Onur Yücel
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, Corrensstr. 3, 48149Münster, Germany
| | - Sebastian Roman Borgert
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, Corrensstr. 3, 48149Münster, Germany
| | - Anja Poehlein
- Georg-August-University Goettingen, Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology and Goettingen Genomics Laboratory, Grisebachstr. 8, 37077, Goettingen, Germany
| | - Karin Niermann
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, Corrensstr. 3, 48149Münster, Germany
| | - Bodo Philipp
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, Corrensstr. 3, 48149Münster, Germany
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421
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Huang C, Leng D, Sun S, Zhang XD. Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection. BMC Genomics 2019; 20:48. [PMID: 30651068 PMCID: PMC6335708 DOI: 10.1186/s12864-019-5429-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 01/02/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Being critically important to the ecosystem, the stability of coral reefs is directly related to the marine and surrounding terrestrial environments. However, coral reefs are now undergoing massive and accelerating devastation due to bleaching. The fact that the breakdown of symbiosis between coral and the dinoflagellate, zooxanthellae, has been well elucidated as the main cause of bleaching, implying the establishment of symbiosis with zooxanthellae plays a crucial role in maintaining coral survival. However, the relevant molecular and cellular mechanisms have not been well studied yet. In this study, based on the deep RNA-sequencing data derived from Mohamed, A. R. et al., an integrated transcriptome analysis was performed to deeply investigate global transcriptome changes of the coral Acropora digitifera in response to infection by dinoflagellate of the genus Symbiodinium. RESULTS The results revealed that compared to RefTranscriptome_v1.0 (A. digitifera transcriptome assembly v1.0), numerous novel transcripts and isoforms were identified, the Symbiodinium-infected coral larvae at 4 h generated the highest proportion of specific isoforms. Alternative splicing analysis showed that intron retention predominated in all alternative transcripts among six statuses. Additionally, 8117 lncRNAs were predicted via a stringent stepwise filtering pipeline. A complex lncRNAs-mRNAs network including 815 lncRNAs and 6395 mRNAs were established, in which 21 lncRNAs were differentially expressed at 4 h post infection. Functional clustering analysis for those differentially lncRNAs-coexpressed mRNAs demonstrated that several biological processes and pathways related to protein kinase activity, metabolic pathways, mitochondrion, ribosome, etc. were enriched. CONCLUSIONS Our study not only refined A. digitifera transcriptome via identification of novel transcripts and isoforms, but also predicted a high-confidence dataset of lncRNAs. Functional study based on the construction of lncRNAs-mRNAs co-expression network has disclosed a complex lncRNA-mediated regulation in response to Symbiodinium infection exhibited in A. digitifera. Once validated, these lncRNAs could be good potential targets for treatment and prevention of bleaching in coral.
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Affiliation(s)
- Chen Huang
- Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Dongliang Leng
- Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Shixue Sun
- Faculty of Health Sciences, University of Macau, Taipa, Macau
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422
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Iniguez AB, Alexe G, Wang EJ, Roti G, Patel S, Chen L, Kitara S, Conway A, Robichaud AL, Stolte B, Bandopadhayay P, Goodale A, Pantel S, Lee Y, Cheff DM, Hall MD, Guha R, Davis MI, Menard M, Nasholm N, Weiss WA, Qi J, Beroukhim R, Piccioni F, Johannessen C, Stegmaier K. Resistance to Epigenetic-Targeted Therapy Engenders Tumor Cell Vulnerabilities Associated with Enhancer Remodeling. Cancer Cell 2018; 34:922-938.e7. [PMID: 30537514 PMCID: PMC6352909 DOI: 10.1016/j.ccell.2018.11.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 09/10/2018] [Accepted: 11/07/2018] [Indexed: 12/26/2022]
Abstract
Drug resistance represents a major challenge to achieving durable responses to cancer therapeutics. Resistance mechanisms to epigenetically targeted drugs remain largely unexplored. We used bromodomain and extra-terminal domain (BET) inhibition in neuroblastoma as a prototype to model resistance to chromatin modulatory therapeutics. Genome-scale, pooled lentiviral open reading frame (ORF) and CRISPR knockout rescue screens nominated the phosphatidylinositol 3-kinase (PI3K) pathway as promoting resistance to BET inhibition. Transcriptomic and chromatin profiling of resistant cells revealed that global enhancer remodeling is associated with upregulation of receptor tyrosine kinases (RTKs), activation of PI3K signaling, and vulnerability to RTK/PI3K inhibition. Large-scale combinatorial screening with BET inhibitors identified PI3K inhibitors among the most synergistic upfront combinations. These studies provide a roadmap to elucidate resistance to epigenetic-targeted therapeutics and inform efficacious combination therapies.
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Affiliation(s)
- Amanda Balboni Iniguez
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
| | - Emily Jue Wang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Giovanni Roti
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; University of Parma Department of Medicine and Surgery, Hematology and BMT, Parma, Italy
| | - Sarvagna Patel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Liying Chen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Samuel Kitara
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amy Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Amanda L Robichaud
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Björn Stolte
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Munich 80337, Germany
| | - Pratiti Bandopadhayay
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amy Goodale
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sasha Pantel
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yenarae Lee
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dorian M Cheff
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rajarshi Guha
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mindy I Davis
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marie Menard
- Departments of Neurology, Neurosurgery, Pediatrics, and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Nicole Nasholm
- Departments of Neurology, Neurosurgery, Pediatrics, and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - William A Weiss
- Departments of Neurology, Neurosurgery, Pediatrics, and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Jun Qi
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Rameen Beroukhim
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Cory Johannessen
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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423
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Engeland WC, Massman L, Mishra S, Yoder JM, Leng S, Pignatti E, Piper ME, Carlone DL, Breault DT, Kofuji P. The Adrenal Clock Prevents Aberrant Light-Induced Alterations in Circadian Glucocorticoid Rhythms. Endocrinology 2018; 159:3950-3964. [PMID: 30321360 PMCID: PMC6240903 DOI: 10.1210/en.2018-00769] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/08/2018] [Indexed: 12/18/2022]
Abstract
The glucocorticoid (GC) rhythm is entrained to light-dark (LD) cycles via a molecular clock in the suprachiasmatic nucleus (SCN) and is maintained by an adrenal clock synchronized by SCN-dependent signals. Targeted deletion of the core clock gene Bmal1 can disrupt adrenal clock function. The requirement of the adrenal clock to stabilize the circadian GC rhythm during exposure to aberrant LD cycles was determined using novel aldosterone synthase (AS)Cre/+::Bmal1Fl/Fl mice in which Bmal1 deletion occurred during postnatal adrenal transdifferentiation. To examine whether adrenal Bmal1 deletion results in loss of the adrenal clock, mice were crossed with mPER2::Luciferase (mPER2Luc/+) mice. Adrenals from ASCre/+::Bmal1+/+::PER2Luc/+ [control (CTRL)] mice show mPER2Luc rhythms ex vivo, whereas slices from ASCre/+::Bmal1Fl/Fl::PER2Luc/+ [knockout (KO)] mice show dampened rhythms. To monitor corticosterone rhythmicity, mice were implanted with subcutaneous microdialysis probes and sampled at 60-minute intervals for up to 3 days under 12:12-hour [τ (T) 24] LD or 3.5:3.5-hour (T7) LD cycles. Corticosterone rhythms were entrained to T24 LD in CTRL and KO mice. Under T7 LD, circadian corticosterone rhythms persisted in most CTRL mice but not KO mice. Hyperadrenocorticism also was observed in KO mice under T7 LD, reflected by increased corticosterone peak amplitude, total daily corticosterone, and responses to ACTH. Analysis of dysregulated adrenal genes in KO mice exposed to aberrant light identified candidates involved in cholesterol metabolism and trafficking, including steroidogenic acute regulatory protein, which could increase steroidogenesis. Our results show that the adrenal clock functions to buffer steroidogenic responses to aberrant light and stabilize circadian GC rhythmicity.
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Affiliation(s)
- William C Engeland
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota
| | - Logan Massman
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota
| | - Shubhendu Mishra
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota
| | - J Marina Yoder
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota
| | - Sining Leng
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Emanuele Pignatti
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mary E Piper
- Harvard Chan Bioinformatics Core, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Diana L Carlone
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - David T Breault
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Paulo Kofuji
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota
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424
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Samarajeewa A, Lenz DR, Xie L, Chiang H, Kirchner R, Mulvaney JF, Edge ASB, Dabdoub A. Transcriptional response to Wnt activation regulates the regenerative capacity of the mammalian cochlea. Development 2018; 145:dev.166579. [PMID: 30389848 PMCID: PMC6288390 DOI: 10.1242/dev.166579] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/25/2018] [Indexed: 01/04/2023]
Abstract
Lack of sensory hair cell (HC) regeneration in mammalian adults is a major contributor to hearing loss. In contrast, the neonatal mouse cochlea retains a transient capacity for regeneration, and forced Wnt activation in neonatal stages promotes supporting cell (SC) proliferation and induction of ectopic HCs. We currently know little about the temporal pattern and underlying mechanism of this age-dependent regenerative response. Using an in vitro model, we show that Wnt activation promotes SC proliferation following birth, but prior to postnatal day (P) 5. This age-dependent decline in proliferation occurs despite evidence that the Wnt pathway is postnatally active and can be further enhanced by Wnt stimulators. Using an in vivo mouse model and RNA sequencing, we show that proliferation in the early neonatal cochlea is correlated with a unique transcriptional response that diminishes with age. Furthermore, we find that augmenting Wnt signaling through the neonatal stages extends the window for HC induction in response to Notch signaling inhibition. Our results suggest that the downstream transcriptional response to Wnt activation, in part, underlies the regenerative capacity of the mammalian cochlea. Summary: Canonical Wnt activation in the mammalian cochlea elicits a unique, age-dependent transcriptional response, which in part regulates the regenerative capacity of supporting cells during cochlear maturation.
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Affiliation(s)
- Anshula Samarajeewa
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto ON, M5S 1A8, Canada
| | - Danielle R Lenz
- Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA.,Eaton-Peabody Laboratory, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Lihong Xie
- Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto ON, M4N 3M5, Canada.,Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning Guangxi, 530021, China
| | - Hao Chiang
- Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA.,Eaton-Peabody Laboratory, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Rory Kirchner
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Joanna F Mulvaney
- Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto ON, M4N 3M5, Canada
| | - Albert S B Edge
- Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA.,Eaton-Peabody Laboratory, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Alain Dabdoub
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto ON, M5S 1A8, Canada .,Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto ON, M4N 3M5, Canada.,Department of Otolaryngology - Head & Neck Surgery, University of Toronto, Toronto ON, M5G 2C4, Canada
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425
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Esteves AM, Graça G, Peyriga L, Torcato IM, Borges N, Portais JC, Santos H. Combined transcriptomics-metabolomics profiling of the heat shock response in the hyperthermophilic archaeon Pyrococcus furiosus. Extremophiles 2018; 23:101-118. [PMID: 30430272 DOI: 10.1007/s00792-018-1065-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/28/2018] [Indexed: 12/25/2022]
Abstract
Pyrococcus furiosus is a remarkable archaeon able to grow at temperatures around 100 °C. To gain insight into how this model hyperthermophile copes with heat stress, we compared transcriptomic and metabolomic data of cells subjected to a temperature shift from 90 °C to 97 °C. In this study, we used RNA-sequencing to characterize the global variation in gene expression levels, while nuclear magnetic resonance (NMR) and targeted ion exchange liquid chromatography-mass spectrometry (LC-MS) were used to determine changes in metabolite levels. Of the 552 differentially expressed genes in response to heat shock conditions, 257 were upregulated and 295 were downregulated. In particular, there was a significant downregulation of genes for synthesis and transport of amino acids. At the metabolite level, 37 compounds were quantified. The level of di-myo-inositol phosphate, a canonical heat stress solute among marine hyperthermophiles, increased considerably (5.4-fold) at elevated temperature. Also, the levels of mannosylglycerate, UDP-N-acetylglucosamine (UDPGlcNac) and UDP-N-acetylgalactosamine were enhanced. The increase in the pool of UDPGlcNac was concurrent with an increase in the transcript levels of the respective biosynthetic genes. This work provides the first metabolomic analysis of the heat shock response of a hyperthermophile.
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Affiliation(s)
- Ana M Esteves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Gonçalo Graça
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Lindsay Peyriga
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France
| | - Inês M Torcato
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Nuno Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Jean-Charles Portais
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France.,Université Paul Sabatier, Université de Toulouse, 31062, Toulouse, France
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal.
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426
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Nilsson MA, Zheng Y, Kumar V, Phillips MJ, Janke A. Speciation Generates Mosaic Genomes in Kangaroos. Genome Biol Evol 2018; 10:33-44. [PMID: 29182740 PMCID: PMC5758907 DOI: 10.1093/gbe/evx245] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2017] [Indexed: 12/22/2022] Open
Abstract
The iconic Australasian kangaroos and wallabies represent a successful marsupial radiation. However, the evolutionary relationship within the two genera, Macropus and Wallabia, is controversial: mitochondrial and nuclear genes, and morphological data have produced conflicting scenarios regarding the phylogenetic relationships, which in turn impact the classification and taxonomy. We sequenced and analyzed the genomes of 11 kangaroos to investigate the evolutionary cause of the observed phylogenetic conflict. A multilocus coalescent analysis using ∼14,900 genome fragments, each 10 kb long, significantly resolved the species relationships between and among the sister-genera Macropus and Wallabia. The phylogenomic approach reconstructed the swamp wallaby (Wallabia) as nested inside Macropus, making this genus paraphyletic. However, the phylogenomic analyses indicate multiple conflicting phylogenetic signals in the swamp wallaby genome. This is interpreted as at least one introgression event between the ancestor of the genus Wallabia and a now extinct ghost lineage outside the genus Macropus. Additional phylogenetic signals must therefore be caused by incomplete lineage sorting and/or introgression, but available statistical methods cannot convincingly disentangle the two processes. In addition, the relationships inside the Macropus subgenus M. (Notamacropus) represent a hard polytomy. Thus, the relationships between tammar, red-necked, agile, and parma wallabies remain unresolvable even with whole-genome data. Even if most methods resolve bifurcating trees from genomic data, hard polytomies, incomplete lineage sorting, and introgression complicate the interpretation of the phylogeny and thus taxonomy.
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Affiliation(s)
- Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Yichen Zheng
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Vikas Kumar
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.,Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
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427
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Checcucci A, diCenzo GC, Ghini V, Bazzicalupo M, Becker A, Decorosi F, Döhlemann J, Fagorzi C, Finan TM, Fondi M, Luchinat C, Turano P, Vignolini T, Viti C, Mengoni A. Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti. ACS Synth Biol 2018; 7:2365-2378. [PMID: 30223644 DOI: 10.1021/acssynbio.8b00158] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbor a multipartite genome composed of more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single genome. Here we report the creation of a genomic hybrid strain in a model multipartite genome species, the plant-symbiotic bacterium Sinorhizobium meliloti. We term this strain as cis-hybrid, since it is produced by genomic material coming from the same species' pangenome. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total genome content) from a donor S. meliloti strain to an acceptor strain. The cis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extracellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modeling were employed for in silico prediction of metabolic flux reorganization. Phenotypes of the cis-hybrid strain were in good agreement with those of both parental strains. Interestingly, the symbiotic phenotype showed a marked cultivar-specific improvement with the cis-hybrid strains compared to both parental strains. These results provide a proof-of-principle for the feasibility of genome-wide replicon-based remodelling of bacterial strains for improved biotechnological applications in precision agriculture.
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Affiliation(s)
- Alice Checcucci
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - George C. diCenzo
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Veronica Ghini
- CERM & CIRMMP, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Marco Bazzicalupo
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Anke Becker
- LOEWE − Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Francesca Decorosi
- Department of Agri-food Production and Environmental Science, University of Florence, 50019 Florence, Italy
| | | | - Camilla Fagorzi
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Marco Fondi
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- CERM & CIRMMP, University of Florence, 50019 Sesto Fiorentino, Italy
- CERM and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Paola Turano
- CERM & CIRMMP, University of Florence, 50019 Sesto Fiorentino, Italy
- CERM and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Tiziano Vignolini
- European Laboratory for Non-Linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
| | - Carlo Viti
- Department of Agri-food Production and Environmental Science, University of Florence, 50019 Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
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428
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Gibson B, Vidgren V, Peddinti G, Krogerus K. Diacetyl control during brewery fermentation via adaptive laboratory engineering of the lager yeast Saccharomyces pastorianus. J Ind Microbiol Biotechnol 2018; 45:1103-1112. [PMID: 30306366 PMCID: PMC6267509 DOI: 10.1007/s10295-018-2087-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/30/2018] [Indexed: 01/12/2023]
Abstract
Diacetyl contributes to the flavor profile of many fermented products. Its typical buttery flavor is considered as an off flavor in lager-style beers, and its removal has a major impact on time and energy expenditure in breweries. Here, we investigated the possibility of lowering beer diacetyl levels through evolutionary engineering of lager yeast for altered synthesis of α-acetolactate, the precursor of diacetyl. Cells were exposed repeatedly to a sub-lethal level of chlorsulfuron, which inhibits the acetohydroxy acid synthase responsible for α-acetolactate production. Initial screening of 7 adapted isolates showed a lower level of diacetyl during wort fermentation and no apparent negative influence on fermentation rate or alcohol yield. Pilot-scale fermentation was carried out with one isolate and results confirmed the positive effect of chlorsulfuron adaptation. Diacetyl levels were over 60% lower at the end of primary fermentation relative to the non-adapted lager yeast and no significant change in fermentation performance or volatile flavor profile was observed due to the adaptation. Whole-genome sequencing revealed a non-synonymous SNP in the ILV2 gene of the adapted isolate. This mutation is known to confer general tolerance to sulfonylurea compounds, and is the most likely cause of the improved tolerance. Adaptive laboratory evolution appears to be a natural, simple and cost-effective strategy for diacetyl control in brewing.
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Affiliation(s)
- Brian Gibson
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, VTT, P.O. Box 1000, FI-02044, Espoo, Finland.
| | - Virve Vidgren
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, VTT, P.O. Box 1000, FI-02044, Espoo, Finland
| | - Gopal Peddinti
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, VTT, P.O. Box 1000, FI-02044, Espoo, Finland
| | - Kristoffer Krogerus
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, VTT, P.O. Box 1000, FI-02044, Espoo, Finland.,Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Kemistintie 1, Aalto, P.O. Box 16100, 00076, Espoo, Finland
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429
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Krogerus K, Preiss R, Gibson B. A Unique Saccharomyces cerevisiae × Saccharomyces uvarum Hybrid Isolated From Norwegian Farmhouse Beer: Characterization and Reconstruction. Front Microbiol 2018; 9:2253. [PMID: 30319573 PMCID: PMC6165869 DOI: 10.3389/fmicb.2018.02253] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/04/2018] [Indexed: 12/04/2022] Open
Abstract
An unknown interspecies Saccharomyces hybrid, "Muri," was recently isolated from a "kveik" culture, a traditional Norwegian farmhouse brewing yeast culture (Preiss et al., 2018). Here we used whole genome sequencing to reveal the strain as an allodiploid Saccharomyces cerevisiae × Saccharomyces uvarum hybrid. Phylogenetic analysis of its sub-genomes revealed that the S. cerevisiae and S. uvarum parent strains of Muri appear to be most closely related to English ale and Central European cider and wine strains, respectively. We then performed phenotypic analysis on a number of brewing-relevant traits in a range of S. cerevisiae, S. uvarum and hybrid strains closely related to the Muri hybrid. The Muri strain possesses a range of industrially desirable phenotypic properties, including broad temperature tolerance, good ethanol tolerance, and efficient carbohydrate use, therefore making it an interesting candidate for not only brewing applications, but potentially various other industrial fermentations, such as biofuel production and distilling. We identified the two S. cerevisiae and S. uvarum strains that were genetically and phenotypically most similar to the Muri hybrid, and then attempted to reconstruct the Muri hybrid by generating de novo interspecific hybrids between these two strains. The de novo hybrids were compared with the original Muri hybrid, and many appeared phenotypically more similar to Muri than either of the parent strains. This study introduces a novel approach to studying hybrid strains and strain development by combining genomic and phenotypic analysis to identify closely related parent strains for construction of de novo hybrids.
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Affiliation(s)
- Kristoffer Krogerus
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, Espoo, Finland
| | - Richard Preiss
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
- Escarpment Laboratories, Guelph, ON, Canada
| | - Brian Gibson
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
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430
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Palodhi A, Ghosh S, Biswas NK, Basu A, Majumder PP, Maitra A. Profiling of genomic alterations of mitochondrial DNA in gingivobuccal oral squamous cell carcinoma: Implications for disease progress. Mitochondrion 2018; 46:361-369. [PMID: 30261279 DOI: 10.1016/j.mito.2018.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 08/08/2018] [Accepted: 09/14/2018] [Indexed: 01/31/2023]
Abstract
We have identified 164 somatic mutations in mitochondrial DNA in gingivobuccal oral cancer by deep sequencing the mitochondrial genome from paired tumor and blood DNA samples from 89 patients. We have found evidence of positive selection of somatic nonsynonymous mutations. Non-synonymous mutations in mitochondrial respiratory genes were found to increase the risk of lymph node metastasis (P = 0.0028). We have observed a significant reduction in mitochondrial DNA copy number in tumor DNA of these patients compared to the DNA from adjacent normal tissue samples (P < 1 × 10-6). Analysis of transcriptome data of tumor and adjacent normal tissue revealed patients harboring mutations in mitochondrial protein-coding genes exhibited reduced expression of mitochondrial transcripts.
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Affiliation(s)
- Arindam Palodhi
- National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
| | - Sahana Ghosh
- National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
| | - Nidhan K Biswas
- National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
| | | | - Arindam Maitra
- National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India.
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431
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Preiss R, Tyrawa C, Krogerus K, Garshol LM, van der Merwe G. Traditional Norwegian Kveik Are a Genetically Distinct Group of Domesticated Saccharomyces cerevisiae Brewing Yeasts. Front Microbiol 2018; 9:2137. [PMID: 30258422 PMCID: PMC6145013 DOI: 10.3389/fmicb.2018.02137] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/21/2018] [Indexed: 01/19/2023] Open
Abstract
The widespread production of fermented food and beverages has resulted in the domestication of Saccharomyces cerevisiae yeasts specifically adapted to beer production. While there is evidence beer yeast domestication was accelerated by industrialization of beer, there also exists a farmhouse brewing culture in western Norway which has passed down yeasts referred to as kveik for generations. This practice has resulted in ale yeasts which are typically highly flocculant, phenolic off flavor negative (POF-), and exhibit a high rate of fermentation, similar to previously characterized lineages of domesticated yeast. Additionally, kveik yeasts are reportedly high-temperature tolerant, likely due to the traditional practice of pitching yeast into warm (>28°C) wort. Here, we characterize kveik yeasts from 9 different Norwegian sources via PCR fingerprinting, whole genome sequencing of selected strains, phenotypic screens, and lab-scale fermentations. Phylogenetic analysis suggests that kveik yeasts form a distinct group among beer yeasts. Additionally, we identify a novel POF- loss-of-function mutation, as well as SNPs and CNVs potentially relevant to the thermotolerance, high ethanol tolerance, and high fermentation rate phenotypes of kveik strains. We also identify domestication markers related to flocculation in kveik. Taken together, the results suggest that Norwegian kveik yeasts are a genetically distinct group of domesticated beer yeasts with properties highly relevant to the brewing sector.
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Affiliation(s)
- Richard Preiss
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
- Escarpment Laboratories, Guelph, ON, Canada
| | - Caroline Tyrawa
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Kristoffer Krogerus
- VTT Technical Research Centre of Finland, Espoo, Finland
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, Espoo, Finland
| | | | - George van der Merwe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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432
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Tomberg K, Westrick RJ, Kotnik EN, Cleuren AC, Siemieniak DR, Zhu G, Saunders TL, Ginsburg D. Whole exome sequencing of ENU-induced thrombosis modifier mutations in the mouse. PLoS Genet 2018; 14:e1007658. [PMID: 30188893 PMCID: PMC6143275 DOI: 10.1371/journal.pgen.1007658] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/18/2018] [Accepted: 08/27/2018] [Indexed: 12/30/2022] Open
Abstract
Although the Factor V Leiden (FVL) gene variant is the most prevalent genetic risk factor for venous thrombosis, only 10% of FVL carriers will experience such an event in their lifetime. To identify potential FVL modifier genes contributing to this incomplete penetrance, we took advantage of a perinatal synthetic lethal thrombosis phenotype in mice homozygous for FVL (F5L/L) and haploinsufficient for tissue factor pathway inhibitor (Tfpi+/-) to perform a sensitized dominant ENU mutagenesis screen. Linkage analysis conducted in the 3 largest pedigrees generated from the surviving F5L/L Tfpi+/- mice ('rescues') using ENU-induced coding variants as genetic markers was unsuccessful in identifying major suppressor loci. Whole exome sequencing was applied to DNA from 107 rescue mice to identify candidate genes enriched for ENU mutations. A total of 3,481 potentially deleterious candidate ENU variants were identified in 2,984 genes. After correcting for gene size and multiple testing, Arl6ip5 was identified as the most enriched gene, though not reaching genome-wide significance. Evaluation of CRISPR/Cas9 induced loss of function in the top 6 genes failed to demonstrate a clear rescue phenotype. However, a maternally inherited (not ENU-induced) de novo mutation (Plcb4R335Q) exhibited significant co-segregation with the rescue phenotype (p = 0.003) in the corresponding pedigree. Thrombosis suppression by heterozygous Plcb4 loss of function was confirmed through analysis of an independent, CRISPR/Cas9-induced Plcb4 mutation (p = 0.01).
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Affiliation(s)
- Kärt Tomberg
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Randal J. Westrick
- Department of Biological Sciences and Center for Data Science and Big Data Analysis, Oakland University, Rochester, Michigan, United States of America
| | - Emilee N. Kotnik
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Audrey C. Cleuren
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David R Siemieniak
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Guojing Zhu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Thomas L. Saunders
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Transgenic Animal Model Core Laboratory, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David Ginsburg
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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433
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Castaño Z, Juan BPS, Spiegel A, Pant A, DeCristo MJ, Laszewski T, Ubellacker JM, Janssen SR, Dongre A, Reinhardt F, Henderson A, del Rio AG, Gifford AM, Herbert Z, Hutchinson JN, Weinberg RA, Chaffer CL, McAllister SS. IL-1β inflammatory response driven by primary breast cancer prevents metastasis-initiating cell colonization. Nat Cell Biol 2018; 20:1084-1097. [PMID: 30154549 PMCID: PMC6511979 DOI: 10.1038/s41556-018-0173-5] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/19/2018] [Indexed: 02/07/2023]
Abstract
Lack of insight into mechanisms governing breast cancer metastasis has precluded the development of curative therapies. Metastasis-initiating cancer cells (MICs) are uniquely equipped to establish metastases, causing recurrence and therapeutic resistance. Using various metastasis models, we discovered that certain primary tumours elicit a systemic inflammatory response involving interleukin-1β (IL-1β)-expressing innate immune cells that infiltrate distant MIC microenvironments. At the metastatic site, IL-1β maintains MICs in a ZEB1-positive differentiation state, preventing MICs from generating highly proliferative E-cadherin-positive progeny. Thus, when the inherent plasticity of MICs is impeded, overt metastases cannot be established. Ablation of the pro-inflammatory response or inhibition of the IL-1 receptor relieves the differentiation block and results in metastatic colonization. Among patients with lymph node-positive breast cancer, high primary tumour IL-1β expression is associated with better overall survival and distant metastasis-free survival. Our data reveal complex interactions that occur between primary tumours and disseminated MICs that could be exploited to improve patient survival.
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Affiliation(s)
- Zafira Castaño
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Beatriz P. San Juan
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Asaf Spiegel
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, 02142, USA
| | - Ayush Pant
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, 02142, USA
| | - Molly J. DeCristo
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Tyler Laszewski
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jessalyn M. Ubellacker
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Susanne R. Janssen
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, 02142, USA
| | - Anushka Dongre
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, 02142, USA
| | - Ferenc Reinhardt
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, 02142, USA
| | - Ayana Henderson
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ana Garcia del Rio
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ann M. Gifford
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, 02142, USA
| | - Zach Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - John N. Hutchinson
- Department of Biostatistics, Harvard T.H. Chan, School of Public Health, Boston, Massachusetts, 02115, USA
| | - Robert A. Weinberg
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, 02142, USA.,MIT Department of Biology and Ludwig/MIT Center for Molecular Oncology, Cambridge, Massachusetts, 02142, USA
| | - Christine L. Chaffer
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, 02142, USA.,Corresponding authors: ,
| | - Sandra S. McAllister
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA,Harvard Stem Cell Institute, Cambridge, Massachusetts, 02138, USA.,Corresponding authors: ,
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434
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Duru IC, Laine P, Andreevskaya M, Paulin L, Kananen S, Tynkkynen S, Auvinen P, Smolander OP. Metagenomic and metatranscriptomic analysis of the microbial community in Swiss-type Maasdam cheese during ripening. Int J Food Microbiol 2018; 281:10-22. [DOI: 10.1016/j.ijfoodmicro.2018.05.017] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 11/28/2022]
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435
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Tay TKY, Guan P, Loke BN, Nasir NDM, Rajasegaran V, Thike AA, Lian D, Chang KTE, Teh BT, Ng CCY, Tan PH. Molecular insights into paediatric breast fibroepithelial tumours. Histopathology 2018; 73:809-818. [PMID: 29969836 DOI: 10.1111/his.13701] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/07/2018] [Accepted: 07/01/2018] [Indexed: 12/13/2022]
Abstract
AIMS This study aims to examine the molecular genetics of paediatric breast fibroepithelial tumours through the targeted sequencing of 50 genes. METHODS AND RESULTS Formalin-fixed paraffin-embedded tissues of fibroepithelial tumours diagnosed in a cohort of patients aged 18 years and below were subjected to next generation sequencing using the Haloplex Target Enrichment System. Twenty-five conventional and 17 juvenile fibroadenomas were studied, with MED12 mutations found in 53.8 and 35% of the tumours, respectively. There was also one benign fibroepithelial neoplasm with hybrid features of juvenile papillomatosis and infarcted benign phyllodes tumour-like areas. Most tumours did not have mutations in well-known cancer driver genes, none harboured TERT promoter mutations, while 25.6% (11 of 43) showed no mutations. Metachronous and synchronous tumours were found to have mutational heterogeneity with some containing mutations in MED12; other genes or no mutations were detected at all. Four of eight giant fibroadenomas (size 5 cm or larger) had no mutations detected, suggesting that there are other molecular mechanisms driving their growth. Tumours with MED12 mutations incidentally had a significantly higher stromal mitotic count compared with those without. CONCLUSION While paediatric fibroepithelial lesions can have cellular stroma potentially raising concern for phyllodes tumour, their lack of TERT promoter and cancer driver mutations is reassuring. The absence of mutations in a significant proportion of tumours, especially the giant fibroadenomas, warrants investigation of pathogenetic mechanisms beyond those involving the 50 genes.
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Affiliation(s)
- Timothy K Y Tay
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Peiyong Guan
- Laboratory of Cancer Epigenome, National Cancer Centre, Singapore
| | - Benjamin N Loke
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Nur Diana M Nasir
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | | | - Aye Aye Thike
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Derrick Lian
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore
| | - Kenneth T E Chang
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, National Cancer Centre, Singapore
| | - Cedric C Y Ng
- Laboratory of Cancer Epigenome, National Cancer Centre, Singapore
| | - Puay-Hoon Tan
- Division of Pathology, Singapore General Hospital, Singapore
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436
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Grillová L, Giacani L, Mikalová L, Strouhal M, Strnadel R, Marra C, Centurion-Lara A, Poveda L, Russo G, Čejková D, Vašků V, Oppelt J, Šmajs D. Sequencing of Treponema pallidum subsp. pallidum from isolate UZ1974 using Anti-Treponemal Antibodies Enrichment: First complete whole genome sequence obtained directly from human clinical material. PLoS One 2018; 13:e0202619. [PMID: 30130365 PMCID: PMC6103504 DOI: 10.1371/journal.pone.0202619] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/07/2018] [Indexed: 12/11/2022] Open
Abstract
Treponema pallidum subsp. pallidum (TPA) is the infectious agent of syphilis, a disease that infects more than 5 million people annually. Since TPA is an uncultivable bacterium, most of the information on TPA genetics comes from genome sequencing and molecular typing studies. This study presents the first complete TPA genome (without sequencing gaps) of clinical isolate (UZ1974), which was obtained directly from clinical material, without multiplication in rabbits. Whole genome sequencing was performed using a newly developed Anti-Treponemal Antibody Enrichment technique combined with previously reported Pooled Segment Genome Sequencing. We identified the UW074B genome, isolated from a sample previously propagated in rabbits, to be the closest relative of the UZ1974 genome and calculated the TPA mutation rate as 2.8 x 10(-10) per site per generation.
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Affiliation(s)
- Linda Grillová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, United States of America
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Radim Strnadel
- Department of Dermatovenerology, University Hospital Brno, Brno, Czech Republic
| | - Christina Marra
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, United States of America
| | - Arturo Centurion-Lara
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, United States of America
| | - Lucy Poveda
- Functional Genomics Center Zurich, University of Zurich, Zurich, Switzerland
| | - Giancarlo Russo
- Functional Genomics Center Zurich, University of Zurich, Zurich, Switzerland
| | - Darina Čejková
- Department of Immunology, Veterinary Research Institute, Brno, Czech Republic
| | - Vladimír Vašků
- 1 Dermatovenereological Clinic St. Anne´s University Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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437
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Zanini S, Šečić E, Jelonek L, Kogel KH. A Bioinformatics Pipeline for the Analysis and Target Prediction of RNA Effectors in Bidirectional Communication During Plant-Microbe Interactions. FRONTIERS IN PLANT SCIENCE 2018; 9:1212. [PMID: 30177942 PMCID: PMC6109766 DOI: 10.3389/fpls.2018.01212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/27/2018] [Indexed: 05/23/2023]
Abstract
Small RNA (sRNA) molecules are key factors in the communication between hosts and their interacting pathogens, where they function as effectors that can modulate both host defense and microbial virulence/pathogenicity through a mechanism termed cross-kingdom RNA interference (ck-RNAi). Consistent with this recent knowledge, sRNAs and their double-stranded RNA precursor have been adopted to control diseases in crop plants, demonstrating a straight forward application of the new findings to approach agricultural problems. Despite the great interest in natural ck-RNAi, it is astonishing to find just a few additional examples in the literature since the first report was published in 2013. One reason might be that the identification of sRNA effectors is hampered both by technical challenges and lack of routine bioinformatics application strategies. Here, we suggest a practical procedure to find, characterize, and validate sRNA effectors in plant-microbe interaction. The aim of this review is not to present and discuss all possible tools, but to give guidelines toward the best established software available for the analysis.
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Affiliation(s)
- Silvia Zanini
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Ena Šečić
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Lukas Jelonek
- Institute of Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
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438
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Comparative Genomic Analysis of Members of the Genera Methanosphaera and Methanobrevibacter Reveals Distinct Clades with Specific Potential Metabolic Functions. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2018; 2018:7609847. [PMID: 30210264 PMCID: PMC6120340 DOI: 10.1155/2018/7609847] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/02/2018] [Indexed: 12/11/2022]
Abstract
Methanobrevibacter and Methanosphaera species represent some of the most prevalent methanogenic archaea in the gastrointestinal tract of animals and humans and play an important role in this environment. The aim of this study was to identify genomic features that are shared or specific for members of each genus with a special emphasis of the analysis on the assimilation of nitrogen and acetate and the utilization of methanol and ethanol for methanogenesis. Here, draft genome sequences of Methanobrevibacter thaueri strain DSM 11995T, Methanobrevibacter woesei strain DSM 11979T, and Methanosphaera cuniculi strain 4103T are reported and compared to those of 16 other Methanobrevibacter and Methanosphaera genomes, including genomes of the 13 currently available types of strains of the two genera. The comparative genome analyses indicate that among other genes, the absence of molybdopterin cofactor biosynthesis is conserved in Methanosphaera species but reveals also that the three species share a core set of more than 300 genes that distinguishes the genus Methanosphaera from the genus Methanobrevibacter. Multilocus sequence analysis shows that the genus Methanobrevibacter can be subdivided into clades, potentially new genera, which may display characteristic specific metabolic features. These features include not only the potential ability of nitrogen fixation and acetate assimilation in a clade comprised of Methanobrevibacter species from the termite gut and Methanobrevibacter arboriphilus strains but also the potential capability to utilize ethanol and methanol in a clade comprising Methanobrevibacter wolinii strain DSM 11976T, Mbb. sp. AbM4, and Mbb. boviskoreani strain DSM 25824T.
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439
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Mangado A, Morales P, Gonzalez R, Tronchoni J. Evolution of a Yeast With Industrial Background Under Winemaking Conditions Leads to Diploidization and Chromosomal Copy Number Variation. Front Microbiol 2018; 9:1816. [PMID: 30127779 PMCID: PMC6088182 DOI: 10.3389/fmicb.2018.01816] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/19/2018] [Indexed: 11/13/2022] Open
Abstract
Industrial wine yeast strains show genome particularities, with strains showing polyploid genomes or chromosome copy number variations, being easier to identify. Although these genomic structures have classically been considered transitory steps in the genomic adaptation to new environmental conditions, they may be more stable than thought. These yeasts are highly specialized strains able to cope with the different stresses associated with the fermentation process, from the high osmolarity to the final ethanol content. In this work, we use adaptive laboratory evolution, focusing on the initial steps of the fermentation process, where growth rate is maximum, to provide new insights into the role of the different genomic and chromosomic rearrangements that occur during adaptation to wine conditions, and providing an understanding of the chronology of the different evolutionary steps.
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Affiliation(s)
- Ana Mangado
- Instituto de Ciencias de la Vid y del Vino, Gobierno de La Rioja, Consejo Superior de Investigaciones Científicas, Universidad de La Rioja, Logroño, Spain
| | - Pilar Morales
- Instituto de Ciencias de la Vid y del Vino, Gobierno de La Rioja, Consejo Superior de Investigaciones Científicas, Universidad de La Rioja, Logroño, Spain
| | - Ramon Gonzalez
- Instituto de Ciencias de la Vid y del Vino, Gobierno de La Rioja, Consejo Superior de Investigaciones Científicas, Universidad de La Rioja, Logroño, Spain
| | - Jordi Tronchoni
- Instituto de Ciencias de la Vid y del Vino, Gobierno de La Rioja, Consejo Superior de Investigaciones Científicas, Universidad de La Rioja, Logroño, Spain
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440
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Shan X, Roberts C, Lan Y, Percec I. Age Alters Chromatin Structure and Expression of SUMO Proteins under Stress Conditions in Human Adipose-Derived Stem Cells. Sci Rep 2018; 8:11502. [PMID: 30065345 PMCID: PMC6068198 DOI: 10.1038/s41598-018-29775-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/14/2018] [Indexed: 12/19/2022] Open
Abstract
Adult stem cells play a critical role in tissue homeostasis and repair. Aging leads to a decline in stem cells’ regenerative capacity that contributes significantly to the maintenance of organ and tissue functions. Age-dependent genomic and epigenetic modifications together play a role in the disruption of critical cellular pathways. However, the epigenetic mechanisms responsible for the decline of adult stem cell functions remain to be well established. Here, we investigated age-dependent, genome-wide alterations in the chromatin accessibility of primary human adipose-derived stem cells (ASCs) in comparison to age-matched fibroblasts via ATAC-seq technology. Our results demonstrate that aging ASCs possess globally more stable chromatin accessibility profiles as compared to aging fibroblasts, suggesting that robust regulatory mechanisms maintain adult stem cell chromatin structure against aging. Furthermore, we observed age-dependent subtle changes in promoter nucleosome positioning in selective pathways during aging, concurrent with altered small ubiquitin-related modifier (SUMO) protein expression under stress conditions. Together, our data suggest a significant role for nucleosome positioning in sumoylation pathway regulation in stress response during adult stem cell aging. The differences described here between the chromatin structure of human ASCs and fibroblasts will further elucidate the mechanisms regulating gene expression during aging in both stem cells and differentiated cells.
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Affiliation(s)
- Xiaoyin Shan
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Cleresa Roberts
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yemin Lan
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ivona Percec
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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441
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Molecular profiling of reticular gigantocellularis neurons indicates that eNOS modulates environmentally dependent levels of arousal. Proc Natl Acad Sci U S A 2018; 115:E6900-E6909. [PMID: 29967172 DOI: 10.1073/pnas.1806123115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Neurons of the medullary reticular nucleus gigantocellularis (NGC) and their targets have recently been a focus of research on mechanisms supporting generalized CNS arousal (GA) required for proper cognitive functions. Using the retro-TRAP method, we characterized transcripts enriched in NGC neurons which have projections to the thalamus. The unique expression and activation of the endothelial nitric oxide (eNOS) signaling pathway in these cells and their intimate connections with blood vessels indicate that these neurons exert direct neurovascular coupling. Production of nitric oxide (NO) within eNOS-positive NGC neurons increases after environmental perturbations, indicating a role for eNOS/NO in modulating environmentally appropriate levels of GA. Inhibition of NO production causes dysregulated behavioral arousal after exposure to environmental perturbation. Further, our findings suggest interpretations for associations between psychiatric disorders and mutations in the eNOS locus.
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442
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Wingfield BD, Liu M, Nguyen HDT, Lane FA, Morgan SW, De Vos L, Wilken PM, Duong TA, Aylward J, Coetzee MPA, Dadej K, De Beer ZW, Findlay W, Havenga M, Kolařík M, Menzies JG, Naidoo K, Pochopski O, Shoukouhi P, Santana QC, Seifert KA, Soal N, Steenkamp ET, Tatham CT, van der Nest MA, Wingfield MJ. Nine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphila, and C. cf. spartinae, pseudomolecules for the pitch canker pathogen Fusarium circinatum, draft genome of Davidsoniella eucalypti, Grosmannia galeiformis, Quambalaria eucalypti, and Teratosphaeria destructans. IMA Fungus 2018; 9:401-418. [PMID: 30622889 PMCID: PMC6317589 DOI: 10.5598/imafungus.2018.09.02.10] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 11/26/2018] [Indexed: 12/14/2022] Open
Abstract
This genome announcement includes draft genomes from Claviceps purpurea s.lat., including C. arundinis, C. humidiphila and C. cf. spartinae. The draft genomes of Davidsoniella eucalypti, Quambalaria eucalypti and Teratosphaeria destructans, all three important eucalyptus pathogens, are presented. The insect associate Grosmannia galeiformis is also described. The pine pathogen genome of Fusarium circinatum has been assembled into pseudomolecules, based on additional sequence data and by harnessing the known synteny within the Fusarium fujikuroi species complex. This new assembly of the F. circinatum genome provides 12 pseudomolecules that correspond to the haploid chromosome number of F. circinatum. These are comparable to other chromosomal assemblies within the FFSC and will enable more robust genomic comparisons within this species complex.
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Affiliation(s)
- Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Miao Liu
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Hai D T Nguyen
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Frances A Lane
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Seamus W Morgan
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - P Markus Wilken
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Janneke Aylward
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Martin P A Coetzee
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Kasia Dadej
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Z Wilhelm De Beer
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Wendy Findlay
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Minette Havenga
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Academy of Sciences of Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Jim G Menzies
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, Manitoba R6M 1Y5, Canada
| | - Kershney Naidoo
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Olivia Pochopski
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Parivash Shoukouhi
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Quentin C Santana
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Keith A Seifert
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Nicole Soal
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Catherine T Tatham
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Margriet A van der Nest
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
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443
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Puente-Sánchez F, Díaz S, Penacho V, Aguilera A, Olsson S. Basis of genetic adaptation to heavy metal stress in the acidophilic green alga Chlamydomonas acidophila. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 200:62-72. [PMID: 29727772 DOI: 10.1016/j.aquatox.2018.04.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 05/26/2023]
Abstract
To better understand heavy metal tolerance in Chlamydomonas acidophila, an extremophilic green alga, we assembled its transcriptome and measured transcriptomic expression before and after Cd exposure in this and the neutrophilic model microalga Chlamydomonas reinhardtii. Genes possibly related to heavy metal tolerance and detoxification were identified and analyzed as potential key innovations that enable this species to live in an extremely acid habitat with high levels of heavy metals. In addition we provide a data set of single orthologous genes from eight green algal species as a valuable resource for comparative studies including eukaryotic extremophiles. Our results based on differential gene expression, detection of unique genes and analyses of codon usage all indicate that there are important genetic differences in C. acidophila compared to C. reinhardtii. Several efflux family proteins were identified as candidate key genes for adaptation to acid environments. This study suggests for the first time that exposure to cadmium strongly increases transposon expression in green algae, and that oil biosynthesis genes are induced in Chlamydomonas under heavy metal stress. Finally, the comparison of the transcriptomes of several acidophilic and non-acidophilic algae showed that the Chlamydomonas genus is polyphyletic and that acidophilic algae have distinctive aminoacid usage patterns.
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MESH Headings
- Actins/genetics
- Actins/metabolism
- Adaptation, Physiological/drug effects
- Cadmium/metabolism
- Cadmium/toxicity
- Carboxylic Ester Hydrolases/classification
- Carboxylic Ester Hydrolases/genetics
- Chlamydomonas/classification
- Chlamydomonas/drug effects
- Chlamydomonas/metabolism
- Dioxygenases/classification
- Dioxygenases/genetics
- Drug Tolerance/genetics
- Metals, Heavy/metabolism
- Metals, Heavy/toxicity
- Phylogeny
- Plant Proteins/classification
- Plant Proteins/genetics
- RNA, Plant/chemistry
- RNA, Plant/isolation & purification
- RNA, Plant/metabolism
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- Sequence Analysis, RNA
- Transcriptome/drug effects
- Water Pollutants, Chemical/chemistry
- Water Pollutants, Chemical/metabolism
- Water Pollutants, Chemical/toxicity
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Affiliation(s)
- Fernando Puente-Sánchez
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Calle Darwin 3, 28049, Madrid, Spain
| | - Silvia Díaz
- Department of Physiology, Genetics and Microbiology, Complutense University of Madrid (UCM), Calle José Antonio Novais 12, 28040 Madrid, Spain
| | - Vanessa Penacho
- Bioarray, S.L. Parque Científico y Empresarial de la UMH, Edificio Quorum III, Avenida de la Universidad s/n, 03202 Elche, Alicante, Spain
| | - Angeles Aguilera
- Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Sanna Olsson
- INIA Forest Research Centre (INIA-CIFOR), Department Forest Ecology and Genetics, Carretera de la Coruña km 7.5, 28040 Madrid, Spain; Department Agricultural Sciences, P.O. Box 27, 00014 University of Helsinki, Finland.
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444
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Genome Sequence of Staphylococcus aureus Ex1, Isolated from a Patient with Spinal Osteomyelitis. GENOME ANNOUNCEMENTS 2018; 6:6/26/e00623-18. [PMID: 29954915 PMCID: PMC6025952 DOI: 10.1128/genomea.00623-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we present the genome sequence of Staphylococcus aureus Ex1, isolated in 2015 from a patient with spinal osteomyelitis at the Royal Devon and Exeter Hospital in the United Kingdom. The availability of the Ex1 genome sequence provides a resource for studying the basis for spinal infection and horizontal gene transfer in S. aureus.
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445
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Lee M, Kim K, Kim SY, Jung SH, Yoon J, Kim MS, Park HC, Jung ES, Chung YJ, Lee SH. Genomic structures of dysplastic nodule and concurrent hepatocellular carcinoma. Hum Pathol 2018; 81:37-46. [PMID: 29949741 DOI: 10.1016/j.humpath.2018.06.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/28/2018] [Accepted: 06/09/2018] [Indexed: 12/19/2022]
Abstract
Although high-grade dysplastic nodule (HGDN) is a preneoplastic lesion that precedes hepatocellular carcinoma (HCC), the genomic structures of HGDN in conjunction with HCC remain elusive. The objective of this study was to identify genomic alterations of HGDN and its difference from HCC that may drive HGDN progression to HCC. We analyzed 16 regions of paired HGDN and HCC from 6 patients using whole-exome sequencing to find somatic mutation and copy number alteration (CNA) profiles of HGDN and HCC. The numbers of mutations, driver mutations, and CNAs of HGDNs were not significantly different from those of HCCs. We identified that the CNA gain of 1q25.3-1q42.13 was predominant in the HCCs compared with that in the HGDNs. Two cases (one nodule-in-nodule case and another case with closely attached HCC and HGDN) showed several overlapped driver mutations (CTNNB1 and CEBPA) and CNAs (losses of CDKN2A, RB1, and TP53) between HGDNs and HCCs, suggesting their roles in the early HCC development. The other 4 cases with spatially separated HCCs and HGDNs showed few overlapped alterations between the paired HCCs and HGDNs. Mutations in ERBB2 and CCND1, and CNAs (gains of CTNNB1, MET, and SMO and losses of PTEN, TP53, and SETD2) were identified as "HCC predominant," suggesting their roles in the progression of HGDN to HCC. Our data show that HCCs are direct descendants of HGDNs in some cases, but there is no direct evidence of such relationship in spatially separated cases. Genomic features of HGDN identified in this study provide a useful resource for dissecting clues for the genetic diagnosis of HGDN and HCC.
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Affiliation(s)
- Minho Lee
- Catholic Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Kyung Kim
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Shinn Young Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Seung-Hyun Jung
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Jonghwan Yoon
- Catholic Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Min Sung Kim
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Hyeon-Chun Park
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Eun Sun Jung
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Yeun-Jun Chung
- Catholic Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea.
| | - Sug Hyung Lee
- Catholic Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea.
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446
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Jung SH, Kim SY, An CH, Lee SH, Jung ES, Park HC, Kim MS, Chung YJ, Lee SH. Clonal Structures of Regionally Synchronous Gastric Adenomas and Carcinomas. Clin Cancer Res 2018; 24:4715-4725. [PMID: 29945994 DOI: 10.1158/1078-0432.ccr-18-0345] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/07/2018] [Accepted: 06/22/2018] [Indexed: 01/11/2023]
Abstract
Purpose: Gastric adenoma (GA) is a premalignant lesion that precedes intestinal-type gastric carcinoma (GC). However, genetic progression mechanisms from GA to GC have not been clarified.Experimental Design: We performed whole-exome sequencing-based mutational analyses for 15 synchronous pairs of attached GAs and GCs.Results: There was no significant difference in the number of driver mutations or copy-number alterations between GAs and GCs. Well-known mutations of TP53, APC, RNF43, and RPL22 were recurrently detected in synchronous GA/GC pairs. In addition, we discovered novel KDM6A, PREX2, FAT1, KMT2C, GLI3, and RPL22 mutations and hypermutation in GAs, but did not identify recurrent drivers for GA-to-GC progression. Clonal structure analyses revealed that most GA/GC pairs exhibit parallel evolution with early divergence rather than stepwise evolution during GA-to-GC progression. Of note, three cases were identified as clonally nonrelated GA/GC pairs despite the lack of histologic differences. We found differences in dominant mutational signatures 1, 6, 15, and 17 in GA/GC trunks, GA branches, and GC branches. Compared with our previous work on synchronous colon adenoma/carcinoma genome structures, where most drivers were in the trunk with parallel evolution, synchronous GA/GC genomes showed a different model of parallel evolution, with many drivers in the branches.Conclusions: The preferred sequence of mutational events during GA-to-GC progression might be more context-dependent than colon adenoma progression. Our results show that nonclonal synchronous GA/GC is common and that GA genomes have already acquired distinct genomic alterations, suggesting caution in the diagnosis of synchronous GA and GC, especially in residual or recurrent cases. Clin Cancer Res; 24(19); 4715-25. ©2018 AACR.
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Affiliation(s)
- Seung-Hyun Jung
- Department of Cancer Evolution Research Center, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea.,Department of Integrated Research Center for Genome Polymorphism, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea
| | - Shin Young Kim
- Department of Integrated Research Center for Genome Polymorphism, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea.,Department of Surgery, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea
| | - Chang Hyeok An
- Department of Surgery, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea
| | - Sung Hak Lee
- Department of Hospital Pathology, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea
| | - Eun Sun Jung
- Department of Hospital Pathology, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea
| | - Hyeon-Chun Park
- Department of Integrated Research Center for Genome Polymorphism, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea
| | - Min Sung Kim
- Department of Cancer Evolution Research Center, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea.,Department of Pathology, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea
| | - Yeun-Jun Chung
- Department of Cancer Evolution Research Center, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea. .,Department of Integrated Research Center for Genome Polymorphism, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea.,Department of Microbiology, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea
| | - Sug Hyung Lee
- Department of Cancer Evolution Research Center, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea. .,Department of Pathology, College of Medicine, the Catholic University of Korea, Seoul, Republic of Korea
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447
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Rosenberg S, Simeonova I, Bielle F, Verreault M, Bance B, Le Roux I, Daniau M, Nadaradjane A, Gleize V, Paris S, Marie Y, Giry M, Polivka M, Figarella-Branger D, Aubriot-Lorton MH, Villa C, Vasiljevic A, Lechapt-Zalcman E, Kalamarides M, Sharif A, Mokhtari K, Pagnotta SM, Iavarone A, Lasorella A, Huillard E, Sanson M. A recurrent point mutation in PRKCA is a hallmark of chordoid gliomas. Nat Commun 2018; 9:2371. [PMID: 29915258 PMCID: PMC6006150 DOI: 10.1038/s41467-018-04622-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 05/14/2018] [Indexed: 12/31/2022] Open
Abstract
Chordoid glioma (ChG) is a characteristic, slow growing, and well-circumscribed diencephalic tumor, whose mutational landscape is unknown. Here we report the analysis of 16 ChG by whole-exome and RNA-sequencing. We found that 15 ChG harbor the same PRKCAD463H mutation. PRKCA encodes the Protein kinase C (PKC) isozyme alpha (PKCα) and is mutated in a wide range of human cancers. However the hot spot PRKCAD463H mutation was not described in other tumors. PRKCAD463H is strongly associated with the activation of protein translation initiation (EIF2) pathway. PKCαD463H mRNA levels are more abundant than wild-type PKCα transcripts, while PKCαD463H is less stable than the PCKαWT protein. Compared to PCKαWT, the PKCαD463H protein is depleted from the cell membrane. The PKCαD463H mutant enhances proliferation of astrocytes and tanycytes, the cells of origin of ChG. In conclusion, our study identifies the hallmark mutation for chordoid gliomas and provides mechanistic insights on ChG oncogenesis. Chordoid glioma is a slow growing diencephalic tumor whose mutational landscape is poorly characterized. Here, the authors perform whole-exome and RNA-sequencing and find that 15 of 16 chordoid glioma cases studied harbor the same PRKCA mutation which results in enhanced proliferation.
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Affiliation(s)
- Shai Rosenberg
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France.,Gaffin Center for Neuro-oncology, Sharett Institute for Oncology, Hadassah - Hebrew University Medical Center, 91120, Jerusalem, Israel
| | - Iva Simeonova
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France
| | - Franck Bielle
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France.,Laboratoire R Escourolle, AP-HP, Hôpital de la Pitié-Salpêtrière, F-75013, Paris, France
| | - Maite Verreault
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France
| | - Bertille Bance
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France
| | - Isabelle Le Roux
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France
| | - Mailys Daniau
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France
| | - Arun Nadaradjane
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France
| | - Vincent Gleize
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France
| | - Sophie Paris
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France
| | - Yannick Marie
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France.,Onconeurotek Tumor Bank, Institut du Cerveau et de la Moelle épinère-ICM, F-75013, Paris, France
| | - Marine Giry
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France
| | - Marc Polivka
- Department of Pathology, AP-HP, Hôpital Lariboisière, F-75010, Paris, France
| | - Dominique Figarella-Branger
- Pathology and Neuropathology Department, Assistance Publique-Hôpitaux de Marseille (AP-HM), CHU Timone, 13005, Marseille, France
| | | | - Chiara Villa
- Department of Pathological Cytology and Anatomy, Foch Hospital, Suresnes, F-92151, Paris, France
| | - Alexandre Vasiljevic
- Centre de Biologie et Pathologie Est, Groupement Hospitalier Est, Hospices Civils de Lyon, 69500, Bron, France
| | - Emmanuèle Lechapt-Zalcman
- Department of Pathology, CHU de Caen, Caen, France Normandie Univ, UNICAEN, CEA, CNRS, ISTCT/LDM-TEP Group, 14000, Caen, France
| | - Michel Kalamarides
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France.,Service de Neurochirurgie, AP-HP, Hôpital de la Pitié-Salpêtrière, F-75013, Paris, France
| | - Ariane Sharif
- INSERM U1172, "Development and Plasticity of the Neuroendocrine Brain", F-59045, Lille, France
| | - Karima Mokhtari
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France.,Laboratoire R Escourolle, AP-HP, Hôpital de la Pitié-Salpêtrière, F-75013, Paris, France
| | - Stefano Maria Pagnotta
- Dipartimento di Scienze e Tecnologie, Università degli Studi del Sannio, 82100, Benevento, Italy.,Institute for Cancer Genetics, Columbia University Medical Center, New York City, NY, 10032, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University Medical Center, New York City, NY, 10032, USA.,Departments of Neurology and Pathology, Institute for Cancer Genetics, Irving Comprehensive Research Center, New York, NY, 10032, USA
| | - Anna Lasorella
- Institute for Cancer Genetics, Columbia University Medical Center, New York City, NY, 10032, USA.,Departments of Pediatrics and Pathology, Institute for Cancer Genetics, Irving Comprehensive Research Center, New York, NY, 10032, USA
| | - Emmanuelle Huillard
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France
| | - Marc Sanson
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, ICM, F-75013, Paris, France. .,Onconeurotek Tumor Bank, Institut du Cerveau et de la Moelle épinère-ICM, F-75013, Paris, France. .,AP-HP, Hôpital de la Pitié-Salpêtrière, Service de Neurologie 2, F-75013, Paris, France. .,Site de Recherche Intégrée sur le Cancer (SiRIC) "CURAMUS", F-75013, Paris, France.
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448
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Yuan Y, Chen S. Widespread antisense transcription of Populus genome under drought. Mol Genet Genomics 2018; 293:1017-1033. [PMID: 29876646 DOI: 10.1007/s00438-018-1456-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 05/31/2018] [Indexed: 12/18/2022]
Abstract
Antisense transcription is widespread in many genomes and plays important regulatory roles in gene expression. The objective of our study was to investigate the extent and functional relevance of antisense transcription in forest trees. We employed Populus, a model tree species, to probe the antisense transcriptional response of tree genome under drought, through stranded RNA-seq analysis. We detected nearly 48% of annotated Populus gene loci with antisense transcripts and 44% of them with co-transcription from both DNA strands. Global distribution of reads pattern across annotated gene regions uncovered that antisense transcription was enriched in untranslated regions while sense reads were predominantly mapped in coding exons. We further detected 1185 drought-responsive sense and antisense gene loci and identified a strong positive correlation between the expression of antisense and sense transcripts. Additionally, we assessed the antisense expression in introns and found a strong correlation between intronic expression and exonic expression, confirming antisense transcription of introns contributes to transcriptional activity of Populus genome under drought. Finally, we functionally characterized drought-responsive sense-antisense transcript pairs through gene ontology analysis and discovered that functional groups including transcription factors and histones were concordantly regulated at both sense and antisense transcriptional level. Overall, our study demonstrated the extensive occurrence of antisense transcripts of Populus genes under drought and provided insights into genome structure, regulation pattern and functional significance of drought-responsive antisense genes in forest trees. Datasets generated in this study serve as a foundation for future genetic analysis to improve our understanding of gene regulation by antisense transcription.
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Affiliation(s)
- Yinan Yuan
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.
| | - Su Chen
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
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449
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Coan RLB, Martins C. Landscape of Transposable Elements Focusing on the B Chromosome of the Cichlid Fish Astatotilapia latifasciata. Genes (Basel) 2018; 9:genes9060269. [PMID: 29882892 PMCID: PMC6027319 DOI: 10.3390/genes9060269] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 12/26/2022] Open
Abstract
B chromosomes (Bs) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). B origin is generally linked to the A-chromosome complement (A). The first report of a B chromosome in African cichlids was in Astatotilapia latifasciata, which can harbor 0, 1, or 2 Bs Classical cytogenetic studies found high a TE content on this B chromosome. In this study, we aimed to understand TE composition and expression in the A. latifasciata genome and its relation to the B chromosome. We used bioinformatics analysis to explore the genomic organization of TEs and their composition on the B chromosome. The bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to that of other cichlid fishes and several expanded elements on its B chromosome. With RNA sequencing data (RNA-seq), we showed that all major TE classes are transcribed in the brain, muscle, and male and female gonads. An evaluation of TE transcription levels between B- and B+ individuals showed that few elements are differentially expressed between these groups and that the expanded B elements are not highly transcribed. Putative silencing mechanisms may act on the B chromosome of A. latifasciata to prevent the adverse consequences of repeat transcription and mobilization in the genome.
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Affiliation(s)
- Rafael L B Coan
- Department of Morphology, Institute of Biosciences, São Paulo State University (UNESP), 18618-689 Botucatu, SP, Brazil.
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences, São Paulo State University (UNESP), 18618-689 Botucatu, SP, Brazil.
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450
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de Barros Damgaard P, Martiniano R, Kamm J, Moreno-Mayar JV, Kroonen G, Peyrot M, Barjamovic G, Rasmussen S, Zacho C, Baimukhanov N, Zaibert V, Merz V, Biddanda A, Merz I, Loman V, Evdokimov V, Usmanova E, Hemphill B, Seguin-Orlando A, Yediay FE, Ullah I, Sjögren KG, Iversen KH, Choin J, de la Fuente C, Ilardo M, Schroeder H, Moiseyev V, Gromov A, Polyakov A, Omura S, Senyurt SY, Ahmad H, McKenzie C, Margaryan A, Hameed A, Samad A, Gul N, Khokhar MH, Goriunova OI, Bazaliiskii VI, Novembre J, Weber AW, Orlando L, Allentoft ME, Nielsen R, Kristiansen K, Sikora M, Outram AK, Durbin R, Willerslev E. The first horse herders and the impact of early Bronze Age steppe expansions into Asia. Science 2018; 360:science.aar7711. [PMID: 29743352 DOI: 10.1126/science.aar7711] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/02/2018] [Indexed: 12/16/2022]
Abstract
The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyzed 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after, but not at the time of, Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia.
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Affiliation(s)
| | - Rui Martiniano
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Jack Kamm
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Guus Kroonen
- Department of Nordic Studies and Linguistics, University of Copenhagen, Copenhagen, Denmark.,Leiden University Centre for Linguistics, Leiden University, Leiden, Netherlands
| | - Michaël Peyrot
- Leiden University Centre for Linguistics, Leiden University, Leiden, Netherlands
| | - Gojko Barjamovic
- Department of Near Eastern Languages and Civilizations, Harvard University, Cambridge, MA, USA
| | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Claus Zacho
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | | | - Victor Zaibert
- Institute of Archaeology and Steppe Civilization, Al-Farabi Kazakh National University, Almaty, 050040, Kazakhstan
| | - Victor Merz
- S. Toraighyrov Pavlodar State University, Joint Research Center for Archeological Studies named after A.Kh. Margulan, Pavlodar, Kazakhstan
| | - Arjun Biddanda
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Ilja Merz
- S. Toraighyrov Pavlodar State University, Joint Research Center for Archeological Studies named after A.Kh. Margulan, Pavlodar, Kazakhstan
| | - Valeriy Loman
- Saryarkinsky Institute of Archaeology, Buketov Karaganda State University, Karaganda. 100074, Kazakhstan
| | - Valeriy Evdokimov
- Saryarkinsky Institute of Archaeology, Buketov Karaganda State University, Karaganda. 100074, Kazakhstan
| | - Emma Usmanova
- Saryarkinsky Institute of Archaeology, Buketov Karaganda State University, Karaganda. 100074, Kazakhstan
| | - Brian Hemphill
- Department of Anthropology, University of Alaska, Fairbanks, AK, USA
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Fulya Eylem Yediay
- The Institute of Forensic Sciences, Istanbul University, Istanbul, Turkey
| | - Inam Ullah
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark.,Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, 40530 Göteborg, Sweden
| | - Katrine Højholt Iversen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jeremy Choin
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Constanza de la Fuente
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Melissa Ilardo
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St. Petersburg, Russia
| | - Andrey Gromov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St. Petersburg, Russia
| | - Andrei Polyakov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Sachihiro Omura
- Japanese Institute of Anatolian Archaeology, Kaman, Kırşehir, Turkey
| | | | - Habib Ahmad
- Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan.,Center of Omic Sciences, Islamia College, Peshawar, Pakistan
| | - Catriona McKenzie
- Department of Archaeology, University of Exeter, Exeter, EX4 4QE, UK
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Abdul Hameed
- Department of Archeology, Hazara University, Garden Campus, Mansehra, Pakistan
| | - Abdul Samad
- Directorate of Archaeology and Museums Government of Khyber Pakhtunkhwa, Pakistan
| | - Nazish Gul
- Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan
| | | | - O I Goriunova
- Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Academician Lavrent'iev Ave. 17, Novosibirsk, 630090, Russia.,Department of History, Irkutsk State University, Karl Marx Street 1, Irkutsk 664003, Russia
| | - Vladimir I Bazaliiskii
- Department of History, Irkutsk State University, Karl Marx Street 1, Irkutsk 664003, Russia
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Andrzej W Weber
- Department of Anthropology, University of Alberta, Edmonton, Alberta, T6G 2H4, Canada
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université deToulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Nielsen
- Departments of Integrative Biology and Statistics, University of Berkeley, Berkeley, CA, USA
| | - Kristian Kristiansen
- Department of Historical Studies, University of Gothenburg, 40530 Göteborg, Sweden
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Alan K Outram
- Department of Archaeology, University of Exeter, Exeter, EX4 4QE, UK
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK. .,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark. .,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.,Department of Zoology, University of Cambridge, Cambridge, UK
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