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Manning JC, Boza JM, Cesarman E, Erickson D. Rapid, equipment-free extraction of DNA from skin biopsies for point-of-care diagnostics. Sci Rep 2024; 14:13782. [PMID: 38877073 PMCID: PMC11178891 DOI: 10.1038/s41598-024-64533-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
Kaposi's sarcoma (KS) is a cancer affecting skin and internal organs for which the Kaposi's sarcoma associated herpesvirus (KSHV) is a necessary cause. Previous work has pursued KS diagnosis by quantifying KSHV DNA in skin biopsies using a point-of-care (POC) device which performs quantitative loop-mediated isothermal amplification (LAMP). These previous studies revealed that extracting DNA from patient biopsies was the rate limiting step in an otherwise rapid process. In this study, a simplified, POC-compatible alkaline DNA extraction, ColdSHOT, was optimized for 0.75 mm human skin punch biopsies. The optimized ColdSHOT extraction consistently produced 40,000+ copies of DNA per 5 µl reaction from 3 mg samples-a yield comparable to standard spin column extractions-within 1 h without significant equipment. The DNA yield was estimated sufficient for KSHV detection from KS-positive patient biopsies, and the LAMP assay was not affected by non-target tissue in the unpurified samples. Furthermore, the yields achieved via ColdSHOT were robust to sample storage in phosphate-buffered saline (PBS) or Tris-EDTA (TE) buffer prior to DNA extraction, and the DNA sample was stable after extraction. The results presented in this study indicate that the ColdSHOT DNA extraction could be implemented to simplify and accelerate the LAMP-based diagnosis of Kaposi's sarcoma using submillimeter biopsy samples.
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Affiliation(s)
- Jason Cade Manning
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Juan Manuel Boza
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Ethel Cesarman
- Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10021, USA
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, 14850, USA.
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14850, USA.
- Cornell University, 369 Upson Hall, Ithaca, NY, 14853, USA.
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2
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Murugesan AC, Kumaragurubaran K, Gunasekaran K, Murugasamy SA, Arunachalam S, Annamalai R, Ragothaman V, Ramaswamy S. Molecular Detection of Hemoplasma in animals in Tamil Nadu, India and Hemoplasma genome analysis. Vet Res Commun 2024; 48:955-968. [PMID: 38032521 DOI: 10.1007/s11259-023-10263-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023]
Abstract
Hemoplasma are small pleomorphic wall-less Gram-positive bacteria that infect erythrocytes of various mammalian hosts. They generally cause asymptomatic or chronic anaemia but occasionally causes overt life-threatening hemolytic anaemia. In the present study, 316 cattle, 115 sheep, 61 goats and 6 buffalo blood samples were collected from various villages or organized farms located in nine districts of Tamil Nadu to detect the hemoplasma by PCR. Overall prevalence of 43.04%, 65.22%, and 44.26% hemoplasma DNA was observed in cattle, sheep and goats, respectively. In total, 21 hemoplasma positive samples were sequenced for 16S rRNA gene which revealed 8 Mycoplasma wenyonii, 11 'Candidatus Mycoplasma haemobos' and one Mycoplasma ovis infection. Sheep blood samples from Chennai district were infected with 'Ca. M. haemobos' whereas sheep sample from Thiruvannamalai district was infected with M. wenyonii. At least 50% genes in the hemoplasma genomes were paralogous genes whose functions were not known. Only 'Ca. M. haemolamae' genome contained one primitive CRISPR system without any cas genes. Antimicrobial resistance genes (ARG) could not be identified in any of the hemoplasma genomes but homologous ARG were identified in all the genomes. Adhesion related gene EF-Tu was detected in all 14 hemoplasma genomes but enolase gene was detected only in 'Ca. M. haemohominis' SWG34-3 genome. This is the first report on the prevalence of hemoplasma infection in cattle, sheep and goat in India.
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Affiliation(s)
- Ananda Chitra Murugesan
- Central University Laboratory, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai, 600051, Tamil Nadu, India.
| | - Karthik Kumaragurubaran
- Department of Veterinary Microbiology, Veterinary College and Research Institute, Udumalpet, 642126, Tamil Nadu, India
| | | | | | | | - Raman Annamalai
- Animal Disease Intelligent Unit, Thiruvannamalai, 606601, Tamil Nadu, India
| | | | - Sridhar Ramaswamy
- Central University Laboratory, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai, 600051, Tamil Nadu, India
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3
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Wanere SS, Phad AP, Jagtap RK, Rawal SK, Pyati PS, Lomate PR. Cost-effective and reliable genomic DNA extraction from plant seedlings for high-throughput genotyping in seed industries. Anal Biochem 2023; 676:115245. [PMID: 37429485 DOI: 10.1016/j.ab.2023.115245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/13/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
Genetic purity of seeds is one of the critical aspects in the seed industry. Molecular seed testing laboratories are utilizing PCR based diagnostic tools for genetic purity analysis. High quality DNA is an essential prerequisite for such analyses. Here, we demonstrate a robust and inexpensive DNA extraction method to isolate genomic DNA from variety of crops. Current method (M2) was compared with four commonly used DNA isolation methods for PCR-based genetic characterization and High Resolution Melt (HRM) based hybridity analysis of cotton, okra, tomato and maize using SSR markers. DNA extracted through current method showed excellent yield and quality as compared to other methods. High quality, PCR ready DNA was isolated within 30-50 min and displayed best results for genetic purity analysis using HRM. In contrast, several genomic DNA samples extracted using other methods were found unsuitable for HRM analysis. Our method can be a perfect choice in seed industry, where thousands of samples are processed every day. Notably, using our method single technician can extract DNA from 96 leaf samples within 30-50 min, at a cost of only $0.11/sample. Overall, current DNA extraction method is a reliable and cost-effective solution for large-scale genotyping experiments in the agricultural industry.
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Affiliation(s)
- Shyamkumar S Wanere
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India
| | - Archana P Phad
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India
| | - Rameshwar K Jagtap
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India
| | - Shuban K Rawal
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India
| | - Prashant S Pyati
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India.
| | - Purushottam R Lomate
- Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India.
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4
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Culturable Diversity of Lichen-Associated Yeasts through Enrichment Strategies. ECOLOGIES 2023. [DOI: 10.3390/ecologies4010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Lichens are symbiotic partnerships between a filamentous fungus and a photosymbiotic “alga”. Studies show that lichens harbor endothallic fungi, but that some taxa have been difficult to isolate from the main filamentous thallus-forming fungus and other faster growing lichenicolous/endothallic fungi. Therefore, we aimed to develop and evaluate liquid yeast-enrichment strategies to (1) isolate lichen-associated yeasts in pure culture, and (2) determine the taxonomic placement and breadth of the diversity of culturable yeasts. Eighty-two lichen samples were collected and washed with distilled water, and healthy thalli were ground up and added to seven different yeast-enrichment broths. Yeast colonies were isolated in pure culture and identified using molecular techniques. Initial isolates were identified using BLASTn analysis, and a taxonomic refinement was completed using PhyML analysis. In total, 215 isolates were obtained. The most prevalently isolated ascomycetous yeasts were within the Dothideomycetes (Aureobasidium, Plowrightia, and Dothiora), while the most frequently isolated basidiomycetous yeasts belonged to the genera Curvibasidium, Sporobolomyces, and Tremella. The generic placements could not be determined for 17 isolates, and in total 25 novel species were recovered. The results of this research indicate that (1) lichen-associated yeasts are diverse, (2) employing liquid enrichment strategies is effective for isolating many of these, and (3) lichen thalli represent a valuable untapped reservoir of diverse and novel yeast species.
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5
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Gotvaldová K, Borovička J, Hájková K, Cihlářová P, Rockefeller A, Kuchař M. Extensive Collection of Psychotropic Mushrooms with Determination of Their Tryptamine Alkaloids. Int J Mol Sci 2022; 23:ijms232214068. [PMID: 36430546 PMCID: PMC9693126 DOI: 10.3390/ijms232214068] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/26/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Since not only psilocybin (PSB) but also PSB-containing mushrooms are used for psychedelic therapy and microdosing, it is necessary to know their concentration variability in wild-grown mushrooms. This article aimed to determine the PSB, psilocin (PS), baeocystin (BA), norbaeocystin (NB), and aeruginascin (AE) concentrations in a large sample set of mushrooms belonging to genera previously reported to contain psychotropic tryptamines. Ultra-high performance liquid chromatography coupled with tandem mass spectrometry was used to quantify tryptamine alkaloids in the mushroom samples. Most mushroom collections were documented by fungarium specimens and/or ITS rDNA/LSU/EF1-α sequencing. Concentrations of five tryptamine alkaloids were determined in a large sample set of 226 fruiting bodies of 82 individual collections from seven mushroom genera. For many mushroom species, concentrations of BA, NB, and AE are reported for the first time. The highest PSB/PS concentrations were found in Psilocybe species, but no tryptamines were detected in the P. fuscofulva and P. fimetaria collections. The tryptamine concentrations in mushrooms are extremely variable, representing a problem for mushroom consumers due to the apparent risk of overdose. The varied cocktail of tryptamines in wild mushrooms could influence the medicinal effect compared to therapy with chemically pure PSB, posing a serious problem for data interpretation.
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Affiliation(s)
- Klára Gotvaldová
- Forensic Laboratory of Biologically Active Substances, Department of Chemistry of Natural Compounds, University of Chemistry and Technology Prague, Technická 5, 166 28 Praha 6—Dejvice, 166 28 Prague, Czech Republic
- Psychedelic Research Centre, National Institute of Mental Health, Topolová 748, 250 67 Klecany, Czech Republic
| | - Jan Borovička
- Nuclear Physics Institute of the Czech Academy of Sciences, Hlavní 130, 250 68 Husinec-Řež, Czech Republic
- Institute of Geology of the Czech Academy of Sciences, Rozvojová 269, 165 00 Praha 6, 165 00 Prague, Czech Republic
| | - Kateřina Hájková
- Forensic Laboratory of Biologically Active Substances, Department of Chemistry of Natural Compounds, University of Chemistry and Technology Prague, Technická 5, 166 28 Praha 6—Dejvice, 166 28 Prague, Czech Republic
- Psychedelic Research Centre, National Institute of Mental Health, Topolová 748, 250 67 Klecany, Czech Republic
| | - Petra Cihlářová
- Forensic Laboratory of Biologically Active Substances, Department of Chemistry of Natural Compounds, University of Chemistry and Technology Prague, Technická 5, 166 28 Praha 6—Dejvice, 166 28 Prague, Czech Republic
- Psychedelic Research Centre, National Institute of Mental Health, Topolová 748, 250 67 Klecany, Czech Republic
| | | | - Martin Kuchař
- Forensic Laboratory of Biologically Active Substances, Department of Chemistry of Natural Compounds, University of Chemistry and Technology Prague, Technická 5, 166 28 Praha 6—Dejvice, 166 28 Prague, Czech Republic
- Psychedelic Research Centre, National Institute of Mental Health, Topolová 748, 250 67 Klecany, Czech Republic
- Correspondence: ; Tel.: +420-220444431
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6
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Comparison of the prevalence, antibiotic resistance patterns, and biofilm formation ability of methicillin-resistant Staphylococcus pseudintermedius in healthy dogs and dogs with skin infections. Vet Res Commun 2022; 47:713-721. [DOI: 10.1007/s11259-022-10032-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
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7
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Miller AN, Karakehian J, Raudabaugh DB. Next-Generation Sequencing of Ancient and Recent Fungarium Specimens. J Fungi (Basel) 2022; 8:932. [PMID: 36135657 PMCID: PMC9503353 DOI: 10.3390/jof8090932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 01/04/2023] Open
Abstract
Fungaria are an unmatched resource for providing genetic data from authoritative, taxonomically-correct fungal species, especially type specimens. These specimens serve to anchor species hypotheses by enabling the correct taxonomic placement of taxa in systematic studies. The DNA from ancient specimens older than 30 years is commonly fragmented, and sometimes highly contaminated by exogenous, non-target fungal DNA, making conventional PCR amplification and Sanger sequencing difficult or impossible. Here, we present the results of DNA extraction, PCR amplification of the ITS2 region, and Illumina MiSeq Nano sequencing of nine recent and 11 ancient specimens, including seven type specimens. The taxa sampled included a range of large and fleshy, to small and tough, or small, melanized specimens of Discina, Gyromitra, Propolis, Stictis, and Xerotrema, with a culture of Lasiosphaeria serving as a positive control. DNA was highly fragmented and in very low quantity for most samples, resulting in inconclusive or incorrect results for all but five samples. Taxonomically-correct sequences were generated from the holotype specimens of G. arctica, G. korshinskii, and G. leucoxantha, from the neotype of G. ussuriensis, and from the positive control. Taxonomic assignments were confirmed through morphology, top BLASTn hits, and maximum likelihood phylogenetic analyses. Though this study was not cost-effective due to the small number of samples submitted and few generating correct sequences, it did produce short DNA barcode fragments for four type specimens that are essential for their correct taxonomic placement in our ongoing systematic studies.
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Affiliation(s)
- Andrew N. Miller
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, 1816 South Oak Street, Champaign, IL 61820, USA
| | - Jason Karakehian
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, 1816 South Oak Street, Champaign, IL 61820, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 South Avenue, Urbana, IL 61801, USA
| | - Daniel B. Raudabaugh
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, 1816 South Oak Street, Champaign, IL 61820, USA
- Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA
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8
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Brandão WQ, da Silva RJ, Mojica-Sánchez LC, Maciel BG, Ratkovski GP, de Melo CP. Use of polypyrrole-polystyrene membranes for extracting DNA from plant tissues. BIOMATERIALS AND BIOSYSTEMS 2022; 7:100060. [PMID: 36824490 PMCID: PMC9934434 DOI: 10.1016/j.bbiosy.2022.100060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 10/16/2022] Open
Abstract
We describe the preparation of a membrane composed of polypyrrole-polystyrene (PPy-PS) and its application in DNA extraction. We adopted the electrospinning technique to prepare polystyrene (PS) membranes, which we used as substrates for incorporating polypyrrole chains through an in situ chemical procedure. As a model system, we initially investigated the use of PPy-PS membranes for the extraction of salmon sperm DNA from aqueous solutions. These studies have shown that the PPy-PS membrane has a maximum adsorption capacity of 236.0 mg of DNA per gram of PPy after 30 min of exposure to a DNA solution (100 mg/L). We incorporated the PPy-PS membranes into centrifugation columns, which we used to carry out experiments for extracting and purification of DNA from curly lettuce leaves. The protocol was initially optimized by first examining the most appropriate concentration of the three components of the lysis buffer (Tris/HCl, NaCl, and EDTA-Na). We then investigated the most adequate volumes of the concentrated surfactant solution (SDS 20%) and that used in the protein and polysaccharide precipitation step (5 M potassium acetate, pH 6.3), factors that directly influence the quality and quantity of the fraction of DNA obtained. For curly lettuce leaves, both in their mature and young stages, the yield and purity of the DNA purified using the PPy-PS membrane were comparable to those obtained using a commercial kit. In both cases, the collected DNA samples presented excellent integrity and quality. These results are suggestive that these composite membranes are competitive with the commercial kits available for the extraction and purification of DNA from plants.
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Affiliation(s)
| | - Romário J da Silva
- Departamento de Física, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | | | | | - Gabriela P Ratkovski
- Departamento de Física, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | - Celso P de Melo
- Pós-Graduação em Ciência de Materiais, Brazil
- Departamento de Física, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
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9
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Borovička J, Braeuer S, Walenta M, Hršelová H, Leonhardt T, Sácký J, Kaňa A, Goessler W. A new mushroom hyperaccumulator: Cadmium and arsenic in the ectomycorrhizal basidiomycete Thelephora penicillata. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154227. [PMID: 35240185 DOI: 10.1016/j.scitotenv.2022.154227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
Fruit-bodies of six Thelephora species (Fungi, Basidiomycota, Thelephoraceae) were analyzed for their trace element concentrations. In Thelephora penicillata, extremely high concentrations of Cd and As were found, followed by highly elevated concentrations of Cu and Zn. The highest accumulation ability was found for Cd with a mean concentration of 1.17 ± 0.37 g kg-1 (dry mass) in fruit-bodies collected from 20 unpolluted sites; the mean As concentration was 0.878 ± 0.242 g kg-1. Furthermore, striking accumulation of Se (923 ± 28 mg kg-1) was found in one sample of T. vialis and elevated concentrations of S were detected in T. palmata (19.6 ± 5.9 g kg-1). The analyzed Thelephora species were sequenced and, based on the Maximum Likelihood phylogenetic analysis (ITS rDNA) of the genus, possible other Thelephora (hyper)accumulators were predicted on the basis of their phylogenetic relationship with the discovered (hyper)accumulators. The striking ability of T. penicillata to accumulate simultaneously Cd, As, Cu, and Zn has no parallel in the Fungal Kingdom and raises the question of a biological importance of metal(loid) hyperaccumulation in mushrooms.
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Affiliation(s)
- Jan Borovička
- Institute of Geology of the Czech Academy of Sciences, Rozvojová 269, 16500 Prague 6, Czech Republic; Nuclear Physics Institute of the Czech Academy of Sciences, Hlavní 130, 25068 Husinec-Řež, Czech Republic.
| | - Simone Braeuer
- University of Graz, Institute of Chemistry, Universitätsplatz 1, 8010 Graz, Austria
| | - Martin Walenta
- University of Graz, Institute of Chemistry, Universitätsplatz 1, 8010 Graz, Austria
| | - Hana Hršelová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tereza Leonhardt
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 3, 166 28 Prague, Czech Republic
| | - Jan Sácký
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 3, 166 28 Prague, Czech Republic
| | - Antonín Kaňa
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Walter Goessler
- University of Graz, Institute of Chemistry, Universitätsplatz 1, 8010 Graz, Austria
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10
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DeKrey DH, Klodd AE, Clark MD, Blanchette RA. Grapevine trunk diseases of cold-hardy varieties grown in Northern Midwest vineyards coincide with canker fungi and winter injury. PLoS One 2022; 17:e0269555. [PMID: 35657987 PMCID: PMC9165834 DOI: 10.1371/journal.pone.0269555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/23/2022] [Indexed: 11/19/2022] Open
Abstract
Grapevine trunk diseases make up a disease complex associated with several vascular fungal pathogenic species. Surveys to characterize the composition of grapevine trunk diseases have been conducted for most major grape growing regions of the world. This study presents a similar survey characterizing the fungi associated with grapevine trunk diseases of cold-hardy interspecific hybrid grape varieties grown nearly exclusively in the atypical harsh winter climate of Northern Midwestern United states vineyards. From the 172 samples collected in 2019, 640 isolates obtained by culturing were identified by ITS sequencing and represent 420 sample-unique taxa. From the 420 representative taxa, opportunistic fungi of the order Diaporthales including species of Cytospora and Diaporthe were most frequently identified. Species of Phaeoacremonium, Paraconiothyrium, and Cadophora were also prevalent. In other milder Mediterranean growing climates, species of Xylariales and Botryosphaeriales are often frequently isolated but in this study they were isolated in small numbers. No Phaeomoniellales taxa were isolated. We discuss the possible compounding effects of winter injury, the pathogens isolated, and management strategies. Additionally, difficulties in researching and understanding the grapevine trunk disease complex are discussed.
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Affiliation(s)
- David H. DeKrey
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Annie E. Klodd
- University of Minnesota Extension, Farmington, Minnesota, United States of America
| | - Matthew D. Clark
- Department of Horticultural Science, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Robert A. Blanchette
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
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11
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Galanis A, Vardakas P, Reczko M, Harokopos V, Hatzis P, Skoulakis EMC, Pavlopoulos GA, Patalano S. Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey. Mol Ecol Resour 2022; 22:2506-2523. [PMID: 35593171 DOI: 10.1111/1755-0998.13626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 02/14/2022] [Accepted: 04/13/2022] [Indexed: 11/26/2022]
Abstract
Honeybees (Apis mellifera) continue to succumb to human and environmental pressures despite their crucial role in providing essential ecosystem services. Owing to their foraging and honey production activities, honeybees form complex relationships with species across all domains, such as plants, viruses, bacteria and other hive pests, making honey a valuable biomonitoring tool for assessing their ecological niche. Thus, the application of honey shotgun metagenomics (SM) has paved the way for a detailed description of the species honeybees interact with. Nevertheless, SM bioinformatics tools and DNA extraction methods rely on resources not necessarily optimized for honey. In this study, we compared five widely used taxonomic classifiers using simulated species communities commonly found in honey. We found that Kraken 2 with a threshold of 0.5 performs best in assessing species distribution. We also optimized a simple NaOH-based honey DNA extraction methodology (Direct-SM), which profiled species seasonal variability similarly to an established column-based DNA extraction approach (SM). Both approaches produce results consistent with melissopalinology analysis describing the botanical landscape surrounding the apiary. Interestingly, we detected a strong stability of the bacteria constituting the core and noncore gut microbiome across seasons, pointing to the potential utility of honey for noninvasive assessment of bee microbiota. Finally, the Direct-SM approach to detect Varroa correlates well with the biomonitoring of mite infestation observed in hives. These observations suggest that Direct-SM methodology has the potential to comprehensively describe honeybee ecological niches and can be tested as a building block for large-scale studies to assess bee health in the field.
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Affiliation(s)
- Anastasios Galanis
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece.,Division of Animal and Human Physiology, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Philippos Vardakas
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece.,Department of Apiculture, Institute of Animal Science, Nea Moudania, Greece
| | - Martin Reczko
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece
| | - Vaggelis Harokopos
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece
| | - Pantelis Hatzis
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece
| | - Efthimios M C Skoulakis
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece
| | - Georgios A Pavlopoulos
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece
| | - Solenn Patalano
- Institute for Fundamental Biomedical Research (IFBR), BSRC 'Alexander Fleming', Vari, Greece
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12
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Holec J, Borovička J, Peintner U, Kolařík M. Towards consolidation of Gymnopilus taxonomy: the case of G. stabilis, G. sapineus, and G. penetrans. Mycol Prog 2022. [DOI: 10.1007/s11557-021-01745-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Delgado G, Miller AN, Hashimoto A, Iida T, Ohkuma M, Okada G. A phylogenetic assessment of Endocalyx (Cainiaceae, Xylariales) with E. grossus comb. et stat. nov. Mycol Prog 2022. [DOI: 10.1007/s11557-021-01759-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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14
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The Epidemiology of Sudden Oak Death Disease Caused by Phytophthora ramorum in a Mixed Bay Laurel-Oak Woodland Provides Important Clues for Disease Management. Pathogens 2022; 11:pathogens11020250. [PMID: 35215194 PMCID: PMC8874385 DOI: 10.3390/pathogens11020250] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/07/2022] [Accepted: 02/12/2022] [Indexed: 11/16/2022] Open
Abstract
Epidemiological models are important for the understanding of disease progression in plants and for the design of control strategies. Phytophthora ramorum, the pathogen responsible for the disease known as Sudden Oak Death, causes lethal infection on several oaks but relies on California bay laurels for transmission. Here, repeated surveys of bay laurels and oaks indicated that bay laurel disease incidence was positively correlated with rainfall, bay laurel density, and an eastern aspect, and negatively correlated with bay laurel basal area. Oak infection only occurred in years when rainfall was higher than the 30-year average, and although infection rates were greater among larger trees, mortality was greater among smaller trees. Additionally, larger oaks closer to infected bay laurels exhibited greater infection rates. Disease incidence differed among sites, and only a fraction of bay laurels were disease superspreaders, while even fewer individuals were refugial trees harboring active infections during dry periods. Based on this study, reducing bay laurel density in denser stands and the number of superspreaders or refugial trees in less dense stands may reduce disease incidence. However, the selective removal of bay laurel trees 0–10 m from oaks is likely to be more effective in preventing infection of specific oaks.
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McEntire MS, Reinhart JM, Cox SK, Keller KA. Single-dose pharmacokinetics of orally administered terbinafine in bearded dragons (Pogona vitticeps) and the antifungal susceptibility patterns of Nannizziopsis guarroi. Am J Vet Res 2021; 83:256-263. [PMID: 34941564 DOI: 10.2460/ajvr.21.02.0023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To identify the antifungal susceptibility of Nanniziopsis guarroi isolates and to evaluate the single-dose pharmacokinetics of orally administered terbinafine in bearded dragons. ANIMALS 8 healthy adult bearded dragons. PROCEDURES 4 isolates of N guarroi were tested for antifungal susceptibility. A compounded oral solution of terbinafine (25 mg/mL [20 mg/kg]) was given before blood (0.2 mL) was drawn from the ventral tail vein at 0, 4, 8, 12, 24, 48, 72, and 96 hours after administration. Plasma terbinafine concentrations were measured with high-performance liquid chromatography. RESULTS The antifungal minimum inhibitory concentrations against N guarroi isolates ranged from 4,000 to > 64,000 ng/mL for fluconazole, 125 to 2,000 ng/mL for itraconazole, 125 to 2,000 ng/mL for ketoconazole, 125 to 1,000 ng/mL for posaconazole, 60 to 250 ng/mL for voriconazole, and 15 to 30 ng/mL for terbinafine. The mean ± SD peak plasma terbinafine concentration in bearded dragons was 435 ± 338 ng/mL at 13 ± 4.66 hours after administration. Plasma concentrations remained > 30 ng/mL for > 24 hours in all bearded dragons and for > 48 hours in 6 of 8 bearded dragons. Mean ± SD terminal half-life following oral administration was 21.2 ± 12.40 hours. CLINICAL RELEVANCE Antifungal susceptibility data are available for use in clinical decision making. Results indicated that administration of terbinafine (20 mg/kg, PO, q 24 to 48 h) in bearded dragons may be appropriate for the treatment of dermatomycoses caused by N guarroi. Clinical studies are needed to determine the efficacy of such treatment.
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Affiliation(s)
- Michael S McEntire
- 1Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Champaign-Urbana, Urbana, IL
| | - Jennifer M Reinhart
- 1Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Champaign-Urbana, Urbana, IL
| | - Sherry K Cox
- 2Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN
| | - Krista A Keller
- 1Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Champaign-Urbana, Urbana, IL
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Goudoudaki S, Milioni A, Kritikou S, Velegraki A, Patrinos GP, Gioula G, Manoussopoulos Y, Kambouris ME. Fast, Scalable, and Practical: An Alkaline DNA Extraction Pipeline for Emergency Microbiomics Biosurveillance. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:484-494. [PMID: 34255557 DOI: 10.1089/omi.2021.0090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Pandemics and environmental crises evident from the first two decades of the 21st century call for methods innovation in biosurveillance and early detection of risk signals in planetary ecosystems. In crises conditions, conventional methods in public health, biosecurity, and environmental surveillance do not work well. In addition, the standard laboratory amenities and procedures may become unavailable, irrelevant, or simply not feasible, for example, owing to disruptions in logistics and process supply chains. The COVID-19 pandemic has been a wakeup call in this sense to reintroduce point-of-need diagnostics with an eye to limited resource settings and biosurveillance solutions. We report here a methodology innovation, a fast, scalable, and alkaline DNA extraction pipeline for emergency microbiomics biosurveillance. We believe that the presented methodology is well poised for effective, resilient, and anticipatory responses to future pandemics and ecological crises while contributing to microbiome science and point-of-need diagnostics in nonelective emergency contexts. The alkaline DNA extraction pipeline can usefully expand the throughput in emergencies by deployment or to allow backup in case of instrumentation failure in vital facilities. The need for distributed public health genomics surveillance is increasingly evident in the 21st century. This study makes a contribution to these ends broadly, and for future pandemic preparedness in particular. We call for innovation in biosurveillance methods that remain important existentially on a planet under pressure from unchecked human growth and breach of the boundaries between human and nonhuman animal habitats.
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Affiliation(s)
- Stavroula Goudoudaki
- Plant Protection Division of Patras, Institute of Industrial and Forage Plants, Patras, Greece
| | - Aphroditi Milioni
- National Collection of Pathogenic Fungi, Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Stavroula Kritikou
- National Collection of Pathogenic Fungi, Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Aristea Velegraki
- National Collection of Pathogenic Fungi, Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - George P Patrinos
- Department of Pharmacy, University of Patras, Patras, Greece.,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Georgia Gioula
- Microbiology Department, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Yiannis Manoussopoulos
- Plant Protection Division of Patras, Institute of Industrial and Forage Plants, Patras, Greece
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Bucher BJ, Muchaamba G, Kamber T, Kronenberg PA, Abdykerimov KK, Isaev M, Deplazes P, Alvarez Rojas CA. LAMP Assay for the Detection of Echinococcus multilocularis Eggs Isolated from Canine Faeces by a Cost-Effective NaOH-Based DNA Extraction Method. Pathogens 2021; 10:pathogens10070847. [PMID: 34357996 PMCID: PMC8308659 DOI: 10.3390/pathogens10070847] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022] Open
Abstract
The detection of Echinococcus multilocularis in infected canids and the environment is pivotal for a better understanding of the epidemiology of alveolar echinococcosis in endemic areas. Necropsy/sedimentation and counting technique remain the gold standard for the detection of canid infection. PCR-based detection methods have shown high sensitivity and specificity, but they have been hardly used in large scale prevalence studies. Loop-mediated isothermal amplification (LAMP) is a fast and simple method to detect DNA with a high sensitivity and specificity, having the potential for field-application. A specific LAMP assay for the detection of E. multilocularis was developed targeting the mitochondrial nad1 gene. A crucial step for amplification-based detection methods is DNA extraction, usually achieved utilising silica-gel membrane spin columns from commercial kits which are expensive. We propose two cost-effective and straightforward methods for DNA extraction, using NaOH (method 1A) and InstaGeneTM Matrix (method 1B), from isolated eggs circumventing the need for commercial kits. The sensitivity of both assays with fox samples was similar (72.7%) with multiplex-PCR using protocol 1A and LAMP using protocol 1B. Sensitivity increased up to 100% when testing faeces from 12 foxes infected with more than 100 intestinal stages of E. multilocularis. For dogs, sensitivity was similar (95.4%) for LAMP and multiplex-PCR using protocol 1B and for both methods when DNA was extracted using protocol 1A (90.9%). The DNA extraction methods used here are fast, cheap, and do not require a DNA purification step, making them suitable for field studies in low-income countries for the prevalence study of E. multilocularis.
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Affiliation(s)
- Barbara J. Bucher
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of Zurich, 8057 Zurich, Switzerland; (B.J.B.); (G.M.); (T.K.); (P.A.K.); (P.D.)
| | - Gillian Muchaamba
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of Zurich, 8057 Zurich, Switzerland; (B.J.B.); (G.M.); (T.K.); (P.A.K.); (P.D.)
| | - Tim Kamber
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of Zurich, 8057 Zurich, Switzerland; (B.J.B.); (G.M.); (T.K.); (P.A.K.); (P.D.)
| | - Philipp A. Kronenberg
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of Zurich, 8057 Zurich, Switzerland; (B.J.B.); (G.M.); (T.K.); (P.A.K.); (P.D.)
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Kubanychbek K. Abdykerimov
- Section of Epidemiology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland;
- Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland
| | - Myktybek Isaev
- Department of Parasitology, Kyrgyz Research Institute of Veterinary Medicine Arstanbek Duisheev, Ministry of Education and Science of the Kyrgyz Republic, Bishkek 720033, Kyrgyzstan;
| | - Peter Deplazes
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of Zurich, 8057 Zurich, Switzerland; (B.J.B.); (G.M.); (T.K.); (P.A.K.); (P.D.)
| | - Cristian A. Alvarez Rojas
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of Zurich, 8057 Zurich, Switzerland; (B.J.B.); (G.M.); (T.K.); (P.A.K.); (P.D.)
- Correspondence:
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Raudabaugh DB, Wells DG, Matheny PB, Hughes KW, Sargent M, Iturriaga T, Miller AN. In Vitro Observations of the Interactions between Pholiota carbonaria and Polytrichum commune and Its Potential Environmental Relevance. Life (Basel) 2021; 11:518. [PMID: 34204923 PMCID: PMC8227111 DOI: 10.3390/life11060518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 11/17/2022] Open
Abstract
Wildfires play a critical role in maintaining biodiversity and shaping ecosystem structure in fire-prone regions, and successional patterns involving numerous plant and fungal species in post-fire events have been elucidated. Evidence is growing to support the idea that some post-fire fungi can form endophytic/endolichenic relationships with plants and lichens. However, no direct observations of fire-associated fungal-moss interactions have been visualized to date. Therefore, physical interactions between a post-fire fungus, Pholiota carbonaria, and a moss, Polytrichum commune, were visually examined under laboratory conditions. Fungal appressoria were visualized on germinating spores and living protonemata within two weeks of inoculation in most growth chambers. Appressoria were pigmented, reddish gold to braun, and with a penetration peg. Pigmented, reddish gold to braun fungal hyphae were associated with living tissue, and numerous mature rhizoids contained fungal hyphae at six months. Inter-rhizoidal hyphae were pigmented and reddish gold to braun, but no structures were visualized on mature gametophyte leaf or stem tissues. Based on our visual evidence and previous work, we provide additional support for P. carbonaria having multiple strategies in how it obtains nutrients from the environment, and provide the first visual documentation of these structures in vitro.
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Affiliation(s)
- Daniel B. Raudabaugh
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA; (D.G.W.); (A.N.M.)
- Department of Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Daniel G. Wells
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA; (D.G.W.); (A.N.M.)
- Department of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA
| | - Patrick B. Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA; (P.B.M.); (K.W.H.)
| | - Karen W. Hughes
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA; (P.B.M.); (K.W.H.)
| | - Malcolm Sargent
- Department of Plant Biology, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA;
| | - Teresa Iturriaga
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA;
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA; (D.G.W.); (A.N.M.)
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van Dyk M, Spies CFJ, Mostert L, Halleen F. Survey of Trunk Pathogens in South African Olive Nurseries. PLANT DISEASE 2021; 105:1630-1639. [PMID: 33100152 DOI: 10.1094/pdis-04-20-0798-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Several fungal trunk pathogens are associated with olive trunk diseases in South Africa. Little is known regarding the inoculum sources of these pathogens in the olive industry, and no specific management strategies are in place. The aim of this study was to investigate the status of olive nurseries in South Africa, with regard to the presence of trunk pathogens in olive plant material, to determine whether nursery material can be considered inoculum sources contributing to long-distance dispersal of these pathogens. Isolations were made from asymptomatic cuttings from mother blocks (stage 1), asymptomatic and symptomatic rooted cuttings (stage 2), and 1- to 2-year-old trees (stage 3) of eight cultivars in two nurseries. Known olive trunk pathogens of Nectriaceae, Diaporthaceae, Botrysphaeriaceae, Togniniaceae, Phaeomoniellaceae, and Pleurostomataceae were recovered. Neofusicoccum australe was detected in a single stage 1 cutting. Stage 3 material showed the highest incidence of fungi from these families, with Pleurostoma richardsiae having the highest incidence in both nurseries (82.2 and 36.7% of the 1- to 2-year-old trees). Phaeoacremonium parasiticum was present in 28.9% of the trees from one nursery (stage 3). The remaining pathogens occurred in ≤13.3% of the material. These results indicate that nursery propagation material from mother blocks harbors low levels of trunk pathogens and that additional infections occur during the nursery process. Management strategies should focus on the prevention and elimination of infections in mother blocks as well as during the propagation process to ensure that pathogen-free material is delivered to producers.
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Affiliation(s)
- Meagan van Dyk
- Plant Protection Division, ARC Infruitec-Nietvoorbij, Stellenbosch 7599, South Africa
- Department of Plant Pathology, University of Stellenbosch, Matieland 7602, South Africa
| | - Christoffel F J Spies
- Plant Protection Division, ARC Infruitec-Nietvoorbij, Stellenbosch 7599, South Africa
- Department of Plant Pathology, University of Stellenbosch, Matieland 7602, South Africa
- ARC-Plant Health and Protection, Stellenbosch 7599, South Africa
| | - Lizel Mostert
- Department of Plant Pathology, University of Stellenbosch, Matieland 7602, South Africa
| | - Francois Halleen
- Plant Protection Division, ARC Infruitec-Nietvoorbij, Stellenbosch 7599, South Africa
- Department of Plant Pathology, University of Stellenbosch, Matieland 7602, South Africa
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Fungi associated with galleries of the emerald ash borer. Fungal Biol 2021; 125:551-559. [PMID: 34140151 DOI: 10.1016/j.funbio.2021.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/16/2020] [Accepted: 02/14/2021] [Indexed: 11/21/2022]
Abstract
The emerald ash borer (EAB) is an exotic forest pest that has killed millions of ash trees in the United States and Canada, resulting in an ecological disaster and billions of dollars in economic losses of urban landscape and forest trees. The beetle was first detected in Michigan in 2002 and has spread through much of the Eastern and Midwestern U.S., reaching Minnesota in 2009. Since then, it has spread across the state and poses a great risk to the more than 1 billion ash trees in Minnesota. The larval stage of EAB creates wounds on trees as they feed on the inner bark, causing disruption of water and sap flow that results in tree death. The fungal community associated with EAB larval galleries is poorly understood and the role these fungi may play in tree death is not known. This study describes fungi isolated from EAB larval galleries sampled throughout the main geographic areas of Minnesota where ash is affected by EAB. Fungal cultures were identified by extracting genomic DNA and sequencing the ITS region of the rDNA. Results from 1126 isolates reveal a diverse assemblage of fungi and three functional guilds comprised of canker pathogens, wood decay, and entomopathogenic fungi. The most common canker-associated genera were Cytospora followed by Phaeoacremonium, Paraconiothyrium, Coniothyrium, Nectria, Diplodia, and Botryosphaeria. Fungi in the Basidiomycota were nearly all wood decay causing fungi and many were species of pioneer colonizing genera including Sistotrema, Irpex, Peniophora, Phlebia and Ganoderma. Some of these fungi seriously affect urban trees, having the potential to cause rapid wood decay resulting in hazardous tree situations. Several entomopathogenic genera with the potential for biological control of EAB were also isolated from galleries. Purpureocillium was the most commonly isolated genus, followed by Beauveria, Clonostachys, Lecanicillium, Akanthomyces, Cordyceps, Microcera, Tolypocladium, and Pochonia. The results identify important fungal functional guilds that are occupying a new niche in ash trees resulting from EAB and include fungi that may accelerate decline in tree health, increase hazard tree situations, or may provide options for biological control of this destructive invasive insect.
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Garbelotto M, Popenuck T, Hall B, Schweigkofler W, Dovana F, Goldstein de Salazar R, Schmidt D, Sims LL. Citizen Science Uncovers Phytophthora ramorum as a Threat to Several Rare or Endangered California Manzanita Species. PLANT DISEASE 2020; 104:3173-3182. [PMID: 33044918 DOI: 10.1094/pdis-03-20-0619-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Sudden Oak Death (SOD) Blitzes consist of yearly surveys led by citizen scientists designed to map the distribution of Phytophthora ramorum, cause of the forest disease called SOD, across northern California. During the 2017 Santa Cruz County SOD Blitz, six rare or endangered Arctostaphylos (manzanita) species were found to be possibly symptomatic for the first time. Symptoms included branch cankers and associated canopy mortality, and affected multiple individuals per species. Isolates of P. ramorum were obtained from each of the six species and, through a 30-day-long inoculation experiment on live plants, Koch's postulates were completed for each one of them, conclusively determining that they all are hosts of this pathogen. Two additional manzanita species were later found to be apparently symptomatic in Marin County. Inoculations on detached branches using an isolate of P. ramorum obtained from one of the six rare species from Santa Cruz County were successful, suggesting that these two species may also be hosts of P. ramorum. Detached leaves of all eight species were also successfully inoculated at the University of California-Berkeley in fall 2018 and then again in spring 2019. In these cases, the same isolate was used for all inoculations, in order to obtain information on the comparative susceptibility of the eight species in question. Both branch and leaf inoculations identified significant interspecific differences in susceptibility. The production of sporangia was low on all species but it was not zero, suggesting that sporulation may cause within-plant and limited across-plant contagion, especially in rainy years.
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Affiliation(s)
- Matteo Garbelotto
- Department of ESPM, University of California, Berkeley, CA 94720, U.S.A
| | - Tina Popenuck
- Department of ESPM, University of California, Berkeley, CA 94720, U.S.A
| | - Brett Hall
- University of California-Santa Cruz Arboretum California Conservation Gardens, Santa Cruz, CA 95064, U.S.A
| | - Wolfgang Schweigkofler
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA 94901, U.S.A
| | - Francesco Dovana
- Department of ESPM, University of California, Berkeley, CA 94720, U.S.A
- Department of Life Sciences and Systems Biology, University of Torino, I-10125 Torino, Italy
| | | | - Doug Schmidt
- Department of ESPM, University of California, Berkeley, CA 94720, U.S.A
| | - Laura Lee Sims
- Department of ESPM, University of California, Berkeley, CA 94720, U.S.A
- School of Ag Sciences and Forestry, Louisiana Tech University, Ruston, LA 71270, U.S.A
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22
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Oliva J, Ridley M, Redondo MA, Caballol M. Competitive exclusion amongst endophytes determines shoot blight severity on pine. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13692] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonàs Oliva
- Department of Crop and Forest Sciences University of Lleida Lleida Spain
- Joint Research Unit CTFC‐AGROTECNIO Lleida Spain
| | - Maia Ridley
- Department of Crop and Forest Sciences University of Lleida Lleida Spain
| | - Miguel A. Redondo
- Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Maria Caballol
- Department of Crop and Forest Sciences University of Lleida Lleida Spain
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El-Korany SM, Helmy OM, El-Halawany AM, Ragab YEM, Zedan HH. Kojic acid repurposing as a pancreatic lipase inhibitor and the optimization of its production from a local Aspergillus oryzae soil isolate. BMC Biotechnol 2020; 20:52. [PMID: 33008398 PMCID: PMC7532584 DOI: 10.1186/s12896-020-00644-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/10/2020] [Indexed: 11/24/2022] Open
Abstract
Background Obesity and its related diseases are increasing worldwide. One of the best therapeutic strategies for obesity management is through the inhibition of pancreatic lipase (PL) enzyme. So far orlistat is the only FDA approved PL inhibitor, but with unpleasant side effects. New efficacious anti-obesity drugs are needed to achieve a successful reduction in the incidence and prevalence of obesity. Many microbial metabolites have PL inhibitory activity. Screening soil inhabitants for PL inhibitors could help in increasing the available anti-obesity drugs. We aimed to isolate and identify alternative PL inhibitors from soil flora. Results We screened the crude mycelial methanolic extracts of 39 soil samples for PL inhibitory activity by the quantitative lipase colorimetric assay, using the substrate p-nitrophenyl palmitate and orlistat as positive control. AspsarO, a PL inhibitor producer, was isolated from an agricultural field soil in Giza, Egypt. It was identified as Aspergillus oryzae using colony morphology, microscopical characteristics, 18S rDNA sequencing, and molecular phylogeny. Increasing the PL inhibitor activity, in AspsarO cultures, from 25.9 ± 2% to 61.4 ± 1.8% was achieved by optimizing the fermentation process using a Placket–Burman design. The dried 100% methanolic fraction of the AspsarO culture had an IC50 of 7.48 μg/ml compared to 3.72 μg/ml for orlistat. It decreased the percent weight gain, significantly reduced the food intake and serum triglycerides levels in high-fat diet-fed Sprague–Dawley rats. Kojic acid, the active metabolite, was identified using several biological guided chromatographic and 1H and 13C NMR techniques and had an IC50 of 6.62 μg/ml. Docking pattern attributed this effect to the interaction of kojic acid with the key amino acids (Lys80, Trp252, and Asn84) in PL enzyme binding site. Conclusion Combining the results of the induced obesity animal model, in silico molecular docking and the lipase inhibitory assay, suggests that kojic acid can be a new therapeutic option for obesity management. Besides, it can lower serum triglycerides in obese patients.
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Affiliation(s)
- Sarah Mohamed El-Korany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Omneya Mohamed Helmy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt.
| | | | | | - Hamdallah Hafez Zedan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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Voto P, Dovana F, Garbelotto M. A revision of the genus Psathyrella, with a focus on subsection Spadiceogriseae. Fungal Syst Evol 2020; 4:97-170. [PMID: 32467909 PMCID: PMC7241683 DOI: 10.3114/fuse.2019.04.08] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Specimens belonging to taxa traditionally assigned to the subsection Spadiceogriseae of the genus Psathyrella were analyzed both morphologically and molecularly. Samples included mainly European collections, selected GenBank accessions, and specimens of various North American taxa described by Smith (1972) and deposited at the Herbarium of the University of Michigan (MICH). Three additional taxa from Africa and Central America were also included. Bayesian and Maximum Likelihood analyses of two loci (ITS and Tef-1α) independently and together supported the monophyletic nature of the subsection Spadiceogriseae, and identified nine statistically supported clades within the subsection. North American and European species often fell within the same clade, suggesting a relatively recent origin of the subsection or human induced intercontinental movement. While this study determines for the first time that the presence of a white veil is diagnostic for the entire subsection, very few morphological traits were associated with individual clades, but clades were often distinctively different in terms of habitat association, suggesting that trophic interactions may have driven the evolution of this group of fungi. Combined, morphological and DNA analyses revealed both expected and unexpected synonymies. The new combinations P. vesiculosa, P. ochrofulva and P. sanjuanensis are proposed, and the new species P. rogersiae is described. New information is provided on the taxonomic status and distribution of several species including P. agrariella, P. albescens, P. atrifolia, P. bivelata, P. fatua, P. kauffmanii, P. aff. kauffmanii, P. incondita, P. infida, P. nitens, P. niveobadia, P. phegophila, P. pseudocorrugis sensu Kits van Waveren, P. subnuda. In total, 13 synonymies were proposed. Based on DNA data, five species of uncertain validity were confirmed as valid, while six species may be ambiguous and may require an in-depth re-analysis. The information gathered in this study was used to generate a key to the species of the subsection Spadiceogriseae.
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Affiliation(s)
- P Voto
- Via Garibaldi 173, 45010 Villadose, Italy
| | - F Dovana
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125, Torino, Italy
| | - M Garbelotto
- Department of Environmental Science, Policy, and Management; University of California, Berkeley, CA 94720, USA
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Blanco AM, Cortés R, Bertucci JI, Soletto L, Sánchez E, Valenciano AI, Cerdá-Reverter JM, Delgado MJ. Brain transcriptome profile after CRISPR-induced ghrelin mutations in zebrafish. FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:1-21. [PMID: 31673996 DOI: 10.1007/s10695-019-00687-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Ghrelin (GRL) is a gut-brain hormone with a role in a wide variety of physiological functions in mammals and fish, which points out the ghrelinergic system as a key element for the appropriate biological functioning of the organism. However, many aspects of the multifunctional nature of GRL remain to be better explored, especially in fish. In this study, we used the CRISPR/Cas9 genome editing technique to generate F0 zebrafish in which the expression of grl is compromised. Then, we employed high-throughput mRNA sequencing (RNA-seq) to explore changes in the brain transcriptome landscape associated with the silencing of grl. The CRISPR/Cas9 technique successfully edited the genome of F0 zebrafish resulting in individuals with considerably lower levels of GRL mRNAs and protein and ghrelin O-acyl transferase (goat) mRNAs in the brain, intestine, and liver compared to wild-type (WT) zebrafish. Analysis of brain transcriptome revealed a total of 1360 differentially expressed genes (DEGs) between the grl knockdown (KD) and WT zebrafish, with 664 up- and 696 downregulated DEGs in the KD group. Functional enrichment analysis revealed that DEGs are highly enriched for terms related to morphogenesis, metabolism (especially of lipids), entrainment of circadian clocks, oxygen transport, apoptosis, and response to stimulus. The present study offers valuable information on the central genes and pathways implicated in functions of GRL, and points out the possible involvement of this peptide in some novel functions in fish, such as apoptosis and oxygen transport.
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Affiliation(s)
- Ayelén Melisa Blanco
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, José Antonio Nováis 12, 28040, Madrid, Spain
- Laboratorio de Fisioloxía Animal, Departamento de Bioloxía Funcional e Ciencias da Saúde, Facultade de Bioloxía and Centro de Investigación Mariña, Universidade de Vigo, Vigo, Spain
| | - Raúl Cortés
- Departamento de Fisiología de Peces y Biotecnología, Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, Ribera de Cabanes, 12595, Torre de la Sal, Castellón, Spain
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O'Higgins, Fábrica, 1990, Santiago, Chile
| | | | - Lucia Soletto
- Departamento de Fisiología de Peces y Biotecnología, Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, Ribera de Cabanes, 12595, Torre de la Sal, Castellón, Spain
| | - Elisa Sánchez
- Departamento de Fisiología de Peces y Biotecnología, Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, Ribera de Cabanes, 12595, Torre de la Sal, Castellón, Spain
| | - Ana Isabel Valenciano
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, José Antonio Nováis 12, 28040, Madrid, Spain
| | - José Miguel Cerdá-Reverter
- Departamento de Fisiología de Peces y Biotecnología, Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, Ribera de Cabanes, 12595, Torre de la Sal, Castellón, Spain.
| | - María Jesús Delgado
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, José Antonio Nováis 12, 28040, Madrid, Spain.
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Ergochromes: Heretofore Neglected Side of Ergot Toxicity. Toxins (Basel) 2019; 11:toxins11080439. [PMID: 31349616 PMCID: PMC6722540 DOI: 10.3390/toxins11080439] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 12/17/2022] Open
Abstract
Ergot, fungal genus Claviceps, are worldwide distributed grass pathogens known for their production of toxic ergot alkaloids (EAs) and the great agricultural impact they have on both cereal crop and farm animal production. EAs are traditionally considered as the only factor responsible for ergot toxicity. Using broad sampling covering 13 ergot species infecting wild or agricultural grasses (including cereals) across Europe, USA, New Zealand, and South Africa we showed that the content of ergochrome pigments were comparable to the content of EAs in sclerotia. While secalonic acids A–C (SAs), the main ergot ergochromes (ECs), are well known toxins, our study is the first to address the question about their contribution to overall ergot toxicity. Based on our and published data, the importance of SAs in acute intoxication seems to be negligible, but the effect of chronic exposure needs to be evaluated. Nevertheless, they have biological activities at doses corresponding to quantities found in natural conditions. Our study highlights the need for a re-evaluation of ergot toxicity mechanisms and further studies of SAs’ impact on livestock production and food safety.
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Comparative clustering and genotyping of Campylobacter jejuni strains isolated from broiler and turkey feces by using RAPD-PCR and ERIC-PCR analysis. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1380-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Comparative restriction enzyme mapping of Campylobacter jejuni isolates from turkeys and broilers based on flaA flagellar gene using HpyF3I endonuclease. Folia Microbiol (Praha) 2018; 64:189-195. [PMID: 30151662 DOI: 10.1007/s12223-018-0643-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 08/21/2018] [Indexed: 10/28/2022]
Abstract
Turkeys and broilers have been identified as important reservoirs for Campylobacter jejuni which is of public health significance. The evaluation of the genotypes among C. jejuni strains within different reservoirs is critical for our understanding of the epidemiology of this infectious agent. The present study aimed to compare the genetic diversity and differences of C. jejuni isolates from turkeys and broilers using flagellin PCR-RFLP typing (flaA typing) technique, in terms of the ease of use and discriminatory power. Sixty C. jejuni isolates were detected biochemically and confirmed by duplex-PCR from turkeys and broilers (30 strains from each bird species). Then, a flaA gene fragment (1725 bp) of C. jejuni isolates was amplified and amplicons were digested with HpyF3I enzyme. Restriction analysis by HpyF3I gave four different flaA patterns (H1, H2, H3, H4) among all tested C. jejuni isolates. In broiler isolates, all four patterns were observed but in turkey isolates, only H2 and H4 patterns were present. The results clearly demonstrated that distribution of the flaA typing patterns differed depending on the host species (broiler/turkey). H1 and H3 flaA types are more prevalent in broiler than turkey isolates, while H2 type is significantly more prevalent within isolates from turkey (p < 0.05). The flaA typing technique by digestion with HpyF3I enzyme can almost give us a clue to the source of infection in local outbreaks.
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Serna-Domínguez MG, Andrade-Michel GY, Arredondo-Bernal HC, Gallou A. Two efficient methods for isolation of high-quality genomic DNA from entomopathogenic fungi. J Microbiol Methods 2018; 148:55-63. [DOI: 10.1016/j.mimet.2018.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/09/2018] [Accepted: 03/22/2018] [Indexed: 10/17/2022]
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Wahl HE, Raudabaugh DB, Bach EM, Bone TS, Luttenton MR, Cichewicz RH, Miller AN. What lies beneath? Fungal diversity at the bottom of Lake Michigan and Lake Superior. JOURNAL OF GREAT LAKES RESEARCH 2018; 44:263-270. [PMID: 29736110 PMCID: PMC5935459 DOI: 10.1016/j.jglr.2018.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fungi are phylogenetically diverse organisms found in nearly every environment as key contributors to the processes of nutrient cycling and decomposition. To date, most fungal diversity has been documented from terrestrial habitats leaving aquatic habitats underexplored. In particular, comparatively little is known about fungi inhabiting freshwater lakes, particularly the benthic zone, which may serve as an untapped resource for fungal biodiversity. Advances in technology allowing for direct sequencing of DNA from environmental samples provide a new opportunity to investigate freshwater benthic fungi. In this study, we employed both culture-dependent and culture-independent methods to evaluate the diversity of fungi in one of the largest freshwater systems on Earth, the North American Laurentian Great Lakes. This study presents the first comprehensive survey of fungi from sediment from Lake Michigan and Lake Superior, resulting in 465 fungal taxa with only 7% of sequence overlap between these two methods. Additionally, culture-independent analyses of the ITS1 and ITS2 regions revealed 49% and 72%, respectively, of the OTUs did not match a described fungal taxonomic group below kingdom Fungi. The low level of sequence overlap between methods and high percentage of fungal taxa that can only be classified at the kingdom level suggests an immense amount of fungal diversity remains to be studied in these aquatic fungal communities.
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Affiliation(s)
- Hannah E. Wahl
- Department of Plant Biology, University of Illinois, 265 Morrill Hall, 505 South Goodwin Avenue, Urbana, IL 61801, USA
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
| | - Daniel B. Raudabaugh
- Department of Plant Biology, University of Illinois, 265 Morrill Hall, 505 South Goodwin Avenue, Urbana, IL 61801, USA
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
| | - Elizabeth M. Bach
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
- Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA
| | - Tiffany S. Bone
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
| | - Mark R. Luttenton
- Biology Department and Annis Water Resources Institute, Grand Valley State University, 1 Campus Drive, Allendale, MI 49401, USA
| | - Robert H. Cichewicz
- Natural Products Discovery Group, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Room 1000, University of Oklahoma, Norman, OK 73019-5251, USA
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
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Krisai-Greilhuber I, Chen Y, Jabeen S, Madrid H, Marincowitz S, Razaq A, Ševčíková H, Voglmayr H, Yazici K, Aptroot A, Aslan A, Boekhout T, Borovička J, Crous PW, Ilyas S, Jami F, Jiang YL, Khalid AN, Kolecka A, Konvalinková T, Norphanphoun C, Shaheen S, Wang Y, Wingfield MJ, Wu SP, Wu YM, Yu JY. Fungal Systematics and Evolution: FUSE 3. SYDOWIA 2017; 69:229-264. [PMID: 29386695 PMCID: PMC5788278 DOI: 10.12905/0380.sydowia69-2017-0229] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The present study introduces seven new species, one new combination, one new variety and several interesting taxonomical notes and/or geographical records. Most of the new taxa are Ascomycetes, but the study also includes a new variety of a Basidiomycete. Novel species include Gyromitra khanspurensis (Discinaceae, Pezizales, Pezizomycetes) from Pakistan growing near Cedrus deoadara and Paramyrothecium guiyangense and Paramyrothecium verruridum (Stachybotriaceae, Hypocreales, Sordariomycetes) both isolated from soil in China. New species from South Africa are Sclerostagonospora elegiae on culm litter of Elegia equisetacea, Sclerostagonospora fusiformis on culm litter of Thamnochortus spicigerus, Sclerostagonospora pinguis on culm litter of Cannomois virgata and Sclerostagonospora sulcata on culm litter of Ischyrolepis subverticellata (Phaeosphaeriaceae, Pleosporales, Dothideomycetes). Hapalocystis berkeleyi var. kickxii with its basionym Hypoxylon kickxii is shown to be a taxon on species level and thus recombined as Hapalocystis kickxii (Sydowiellaceae, Diaporthales, Sordariomycetes), and it is lecto- and epitypified. The new variety Pluteus romellii var. luteoalbus (Pluteaceae, Agaricales, Agaricomycetes) growing on a mossy fallen stem of a deciduous tree is described from Czech Republic. Cortinarius scaurocaninus (Cortinariaceae, Agaricales, Agaricomycetes) is new for Austria, Humicola grisea (Chaetomiaceae, Sordariales, Sordariomycetes) is an interesting new record for Chile. Two taxa are reported as new for Turkey: the lichenicolous fungus Opegrapha parasitica (Opegraphaceae, Arthoniales, Arthoniomycetes) growing partly immersed in the thallus of Aspicilia and the lichen Rinodina zwackhiana (Physciaceae, Teloschistales, Lecanoromycetes) from calcareous rock. Finally, Xerula strigosa (Physalacriaceae, Agaricales, Agaricomycetes), described from China, is confirmed to be present also in Pakistan.
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Affiliation(s)
| | - Yun Chen
- Dept. of Plant Pathology, Agricultural College of Guizhou University, Huaxi District, Guiyang City, Guizhou Province 550025, China
- Law Enforcement of Agricultural Bureau, Xiu Wen district, Guiyang city, Guizhou Province 550200, China
| | - Sana Jabeen
- Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Hugo Madrid
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor de Chile, Camino La Pirámide 5750, Huechuraba, Santiago, Chile
| | - Seonju Marincowitz
- Dept. of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P.O. Box X20, Pretoria 0028, South Africa
| | - Abdul Razaq
- Discipline of Botany, Faculty of Fisheries and Wildlife, University of Veterinary and Animal Sciences (UVAS), Ravi Campus, Pattoki, Pakistan
| | - Hana Ševčíková
- Moravian Museum, Department of Botany, Zelný trh 6, 659 37 Brno, Czech Republic
| | - Hermann Voglmayr
- Dept. of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Wien, Austria
| | - Kenan Yazici
- Biology Department, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - André Aptroot
- ABL Herbarium, G.v.d.Veenstraat 107 NL-3762 XK Soest, The Netherlands
| | - Ali Aslan
- Faculty of Pharmacy, Yüzüncü Yıl University, Van, Turkey
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Centre, Uppsalalaan 8, Utrecht, The Netherlands
| | - Jan Borovička
- Institute of Geology of the Czech Academy of Sciences, Rozvojová 256, 165 00 Praha 6, Czech Republic
- Nuclear Physics Institute of the Czech Academy of Sciences, Hlavní 130, 250 68 Husinec-Řež, Czech Republic
| | - Pedro W Crous
- Dept. of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P.O. Box X20, Pretoria 0028, South Africa
- Westerdijk Fungal Biodiversity Centre, Uppsalalaan 8, Utrecht, The Netherlands
| | - Sobia Ilyas
- Dept. of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Fahimeh Jami
- Dept. of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P.O. Box X20, Pretoria 0028, South Africa
| | - Yu-Lan Jiang
- Dept. of Plant Pathology, Agricultural College of Guizhou University, Huaxi District, Guiyang City, Guizhou Province 550025, China
| | - Abdul Nasir Khalid
- Dept. of Botany, University of the Punjab, Quaid-e-Azam Campus-54590, Lahore, Punjab, Pakistan
| | - Anna Kolecka
- Westerdijk Fungal Biodiversity Centre, Uppsalalaan 8, Utrecht, The Netherlands
| | - Tereza Konvalinková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Chada Norphanphoun
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
| | - Shabnum Shaheen
- Dept. of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Yong Wang
- Dept. of Plant Pathology, Agricultural College of Guizhou University, Huaxi District, Guiyang City, Guizhou Province 550025, China
| | - Michael J Wingfield
- Dept. of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P.O. Box X20, Pretoria 0028, South Africa
| | - Shi-Ping Wu
- Guizhou Institute of Plant Protection, Guiyang City 550006, Guizhou Province, China
| | - Yue-Ming Wu
- Dept. of Plant Pathology, Shandong Agricultural University, Taian, 271018, China
| | - Jie-Ying Yu
- Plant Protection and Quarantine Station of Guiyang, Guiyang 550081, Guizhou Province, China
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Staji H, Zandiar L. Importance of Wild Species Kept in Captivity as Reservoirs of Salmonella Serotypes for Human in Petting Exhibitions and Zoo in Iran with Focus on Antimicrobial Resistance. MACEDONIAN VETERINARY REVIEW 2017. [DOI: 10.1515/macvetrev-2017-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Salmonella spp. is the leading cause of zoonotic enteric diseases wich represents a public health concern worldwide. The incidence of zoo-associated salmonellosis is rather high due to the high prevalence and shedding of this bacterium from wild animals specially kept in stressful conditions. To determine the potential public health risk presented by zoo animals in Semnan, we investigated the prevalence of Salmonella serovars Enteritidis and Typhimurium among wild animal species kept in the zoo and pet shops. Totally, 152 fecal samples from species in the zoo and pet shops were collected and Salmonella prevalence and identification was assessed via standard bacteriologic culture methods, serotyping, multiplex-PCR and antimicrobial susceptibility testing. Overall, 21% (32/152) of the samples were confirmed positive for Salmonella and serotyping showed 12.5% (19/32) Salmonella serovar Enteritidis and 8.5% (13/32) serovar Typhimurium, respectively. All the Salmonella isolates were sensitive to Chloramphenicole, Flurefenicole, Meropenem, Ceftizoxime, Imipenem and Ampicillin, while resistance was observed in the case of Nalidixic acid (78%) as the highest resistance, Streptomycin (28%), Oxytetracycline, Neomycin, Furazolidone (each one 15%) and Lincospectin (9.3%). The high occurrence of multidrug resistance Salmonella in zoo and pet animals represents a potential threat to public health and requires strict surveillance and application of hygienic criteria.
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Affiliation(s)
- Hamid Staji
- Department of Pathobiology, Faculty of Veterinary Medicine , Semnan University , Semnan , Iran (Islamic Republic of)
| | - Ladan Zandiar
- Veterinary Medicine Laboratory Student , Semnan University , Semnan , Iran (Islamic Republic of)
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Kozanitas M, Osmundson TW, Linzer R, Garbelotto M. Interspecific interactions between the Sudden Oak Death pathogen Phytophthora ramorum and two sympatric Phytophthora species in varying ecological conditions. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Barge EG, Cripps CL, Osmundson TW. Systematics of the ectomycorrhizal genusLactariusin the Rocky Mountain alpine zone. Mycologia 2017; 108:414-40. [DOI: 10.3852/15-177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 12/02/2015] [Indexed: 11/10/2022]
Affiliation(s)
| | - Cathy L. Cripps
- Plant Science and Plant Pathology Department, Montana State University, Bozeman, Montana 59717
| | - Todd W. Osmundson
- Biology Department, University of Wisconsin–La Crosse, La Crosse, Wisconsin 54601
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Lee HB, Schwab TL, Koleilat A, Ata H, Daby CL, Cervera RL, McNulty MS, Bostwick HS, Clark KJ. Allele-Specific Quantitative PCR for Accurate, Rapid, and Cost-Effective Genotyping. Hum Gene Ther 2016; 27:425-35. [PMID: 26986823 PMCID: PMC4931339 DOI: 10.1089/hum.2016.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Customizable endonucleases such as transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) enable rapid generation of mutant strains at genomic loci of interest in animal models and cell lines. With the accelerated pace of generating mutant alleles, genotyping has become a rate-limiting step to understanding the effects of genetic perturbation. Unless mutated alleles result in distinct morphological phenotypes, mutant strains need to be genotyped using standard methods in molecular biology. Classic restriction fragment length polymorphism (RFLP) or sequencing is labor-intensive and expensive. Although simpler than RFLP, current versions of allele-specific PCR may still require post-polymerase chain reaction (PCR) handling such as sequencing, or they are more expensive if allele-specific fluorescent probes are used. Commercial genotyping solutions can take weeks from assay design to result, and are often more expensive than assembling reactions in-house. Key components of commercial assay systems are often proprietary, which limits further customization. Therefore, we developed a one-step open-source genotyping method based on quantitative PCR. The allele-specific qPCR (ASQ) does not require post-PCR processing and can genotype germline mutants through either threshold cycle (Ct) or end-point fluorescence reading. ASQ utilizes allele-specific primers, a locus-specific reverse primer, universal fluorescent probes and quenchers, and hot start DNA polymerase. Individual laboratories can further optimize this open-source system as we completely disclose the sequences, reagents, and thermal cycling protocol. We have tested the ASQ protocol to genotype alleles in five different genes. ASQ showed a 98-100% concordance in genotype scoring with RFLP or Sanger sequencing outcomes. ASQ is time-saving because a single qPCR without post-PCR handling suffices to score genotypes. ASQ is cost-effective because universal fluorescent probes negate the necessity of designing expensive probes for each locus.
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Affiliation(s)
- Han B Lee
- 1 Neurobiology of Disease Graduate Program, Mayo Graduate School , Rochester, Minnesota
| | - Tanya L Schwab
- 2 Department of Biochemistry and Molecular Biology, Mayo Clinic , Rochester, Minnesota
| | - Alaa Koleilat
- 3 Clinical and Translational Science Graduate Program, Mayo Graduate School , Rochester, Minnesota
| | - Hirotaka Ata
- 3 Clinical and Translational Science Graduate Program, Mayo Graduate School , Rochester, Minnesota.,4 Medical Scientist Training Program, Mayo Graduate School , Rochester, Minnesota
| | - Camden L Daby
- 2 Department of Biochemistry and Molecular Biology, Mayo Clinic , Rochester, Minnesota
| | - Roberto Lopez Cervera
- 2 Department of Biochemistry and Molecular Biology, Mayo Clinic , Rochester, Minnesota
| | - Melissa S McNulty
- 2 Department of Biochemistry and Molecular Biology, Mayo Clinic , Rochester, Minnesota
| | - Hannah S Bostwick
- 2 Department of Biochemistry and Molecular Biology, Mayo Clinic , Rochester, Minnesota
| | - Karl J Clark
- 1 Neurobiology of Disease Graduate Program, Mayo Graduate School , Rochester, Minnesota.,2 Department of Biochemistry and Molecular Biology, Mayo Clinic , Rochester, Minnesota.,3 Clinical and Translational Science Graduate Program, Mayo Graduate School , Rochester, Minnesota
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Staji H, Khoshgoftar J, Javaheri Vayeghan A, Salimi Bejestani MR. Phylogenetic Grouping and Assessment of Virulence Genotypes, With Antibiotic Resistance Patterns, of Escherichia Coli Strains Implicated in Female Urinary Tract Infections. INTERNATIONAL JOURNAL OF ENTERIC PATHOGENS 2016. [DOI: 10.17795/ijep31609] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Gonthier P, Sillo F, Lagostina E, Roccotelli A, Cacciola OS, Stenlid J, Garbelotto M. Selection processes in simple sequence repeats suggest a correlation with their genomic location: insights from a fungal model system. BMC Genomics 2015; 16:1107. [PMID: 26714466 PMCID: PMC4696308 DOI: 10.1186/s12864-015-2274-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Adaptive processes shape the evolution of genomes and the diverse functions of different genomic regions are likely to have an impact on the trajectory and outcome of this evolution. The main underlying hypothesis of this study is that the evolution of Simple Sequence Repeats (SSRs) is correlated with the evolution of the genomic region in which they are located, resulting in differences of motif size, number of repeats, and levels of polymorphisms. These differences should be clearly detectable when analyzing the frequency and type of SSRs within the genome of a species, when studying populations within a species, and when comparing closely related sister taxa. By coupling a genome-wide SSR survey in the genome of the plant pathogenic fungus Heterobasidion irregulare with an analysis of intra- and interspecific variability of 39 SSR markers in five populations of the two sibling species H. irregulare and H. annosum, we investigated mechanisms of evolution of SSRs. RESULTS Results showed a clear dominance of trirepeats and a selection against other repeat number, i.e. di- and tetranucleotides, both in regions inside Open Reading Frames (ORFs) and upstream 5' untranslated region (5'UTR). Locus per locus AMOVA showed SSRs both inside ORFs and upstream 5'UTR were more conserved within species compared to SSRs in other genomic regions, suggesting their evolution is constrained by the functions of the regions they are in. Principal coordinates analysis (PCoA) indicated that even if SSRs inside ORFs were less polymorphic than those in intergenic regions, they were more powerful in differentiating species. These findings indicate SSRs evolution undergoes a directional selection pressure comparable to that of the ORFs they interrupt and to that of regions involved in regulatory functions. CONCLUSIONS Our work linked the variation and the type of SSRs with regions upstream 5'UTR, putatively harbouring regulatory elements, and shows that the evolution of SSRs might be affected by their location in the genome. Additionally, this study provides a first glimpse on a possible molecular basis for fast adaptation to the environment mediated by SSRs.
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Affiliation(s)
- Paolo Gonthier
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095, Grugliasco, Italy.
| | - Fabiano Sillo
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095, Grugliasco, Italy.
| | - Elisa Lagostina
- Department of Environmental Sciences, Policy and Management, University of California at Berkeley, CA, 94720, Berkeley, USA. .,Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy.
| | - Angela Roccotelli
- Department of Environmental Sciences, Policy and Management, University of California at Berkeley, CA, 94720, Berkeley, USA. .,Department of Agriculture, Mediterranean University of Reggio Calabria, 89122, Reggio Calabria, Italy.
| | - Olga Santa Cacciola
- Department of Agriculture, Food and Environment, University of Catania, 95123, Catania, Italy.
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden.
| | - Matteo Garbelotto
- Department of Environmental Sciences, Policy and Management, University of California at Berkeley, CA, 94720, Berkeley, USA.
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Allender MC, Raudabaugh DB, Gleason FH, Miller AN. The natural history, ecology, and epidemiology of Ophidiomyces ophiodiicola and its potential impact on free-ranging snake populations. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2015.05.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Eyre CA, Garbelotto M. Detection, Diversity, and Population Dynamics of Waterborne Phytophthora ramorum Populations. PHYTOPATHOLOGY 2015; 105:57-68. [PMID: 25026455 DOI: 10.1094/phyto-07-13-0196-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Sudden oak death, the tree disease caused by Phytophthora ramorum, has significant environmental and economic impacts on natural forests on the U.S. west coast, plantations in the United Kingdom, and in the worldwide nursery trade. Stream baiting is vital for monitoring and early detection of the pathogen in high-risk areas and is performed routinely; however, little is known about the nature of water-borne P. ramorum populations. Two drainages in an infested California forest were monitored intensively using stream-baiting for 2 years between 2009 and 2011. Pathogen presence was determined both by isolation and polymerase chain reaction (PCR) from symptomatic bait leaves. Isolates were analyzed using simple sequence repeats to study population dynamics and genetic structure through time. Isolation was successful primarily only during spring conditions, while PCR extended the period of pathogen detection to most of the year. Water populations were extremely diverse, and changed between seasons and years. A few abundant genotypes dominated the water during conditions considered optimal for aerial populations, and matched those dominant in aerial populations. Temporal patterns of genotypic diversification and evenness were identical among aerial, soil, and water populations, indicating that all three substrates are part of the same epidemiological cycle, strongly influenced by rainfall and sporulation on leaves. However, there was structuring between substrates, likely arising due to reduced selection pressure in the water. Additionally, water populations showed wholesale mixing of genotypes without the evident spatial autocorrelation present in leaf and soil populations.
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An improved protocol for the isolation of total genomic DNA from Labyrinthulomycetes. Biotechnol Lett 2014; 37:685-90. [PMID: 25355522 DOI: 10.1007/s10529-014-1712-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/21/2014] [Indexed: 10/24/2022]
Abstract
Many protocols have been used for extraction of DNA from Thraustochytrids. These generally involve the use of CTAB, phenol/chloroform and ethanol. They also feature mechanical grinding, sonication, N2 freezing or bead beating. However, the resulting chemical and physical damage to extracted DNA reduces its quality. The methods are also unsuitable for large numbers of samples. Commercially-available DNA extraction kits give better quality and yields but are expensive. Therefore, an optimized DNA extraction protocol was developed which is suitable for Thraustochytrids to both minimise expensive and time-consuming steps prior to DNA extraction and also to improve the yield. The most effective method is a combination of single bead in TissueLyser (Qiagen) and Proteinase K. Results were conclusive: both the quality and the yield of extracted DNA were higher than with any other method giving an average yield of 8.5 µg/100 mg biomass.
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Eyre CA, Kozanitas M, Garbelotto M. Population dynamics of aerial and terrestrial populations of Phytophthora ramorum in a California forest under different climatic conditions. PHYTOPATHOLOGY 2013; 103:1141-1152. [PMID: 23745672 DOI: 10.1094/phyto-11-12-0290-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Limited information is available on how soil and leaf populations of the sudden oak death pathogen, Phytophthora ramorum, may differ in their response to changing weather conditions, and their corresponding role in initiating the next disease cycle after unfavorable weather conditions. We sampled and cultured from 425 trees in six sites, three times at the end of a 3-year-long drought and twice during a wet year that followed. Soil was also sampled twice with similar frequency and design used for sampling leaves. Ten microsatellites were used for genetic analyses on cultures from successful isolations. Results demonstrated that incidence of leaf infection tripled at the onset of the first wet period in 3 years in spring 2010, while that of soil populations remained unchanged. Migration of genotypes among sites was low and spatially limited under dry periods but intensity and range of migration of genotypes significantly increased for leaf populations during wet periods. Only leaf genotypes persisted significantly between years, and genotypes present in different substrates distributed differently in soil and leaves. We conclude that epidemics start rapidly at the onset of favorable climatic conditions through highly transmissible leaf genotypes, and that soil populations are transient and may be less epidemiologically relevant than previously thought.
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